Disclaimer: Neon Genesis Evangelion is the creation of Anno and Gainax. I don't own it, make no claims to it, and am making no profit from the fan fiction. No infringement of copyright is intended. In other words, please don't sue.

Disclaimer: I do not own DC Comics or anything associated with it, and I am making no profit from this fan fiction. No infringement of copyright is intended. In other words, please don't sue.

Chapter Two: Final Fate

Shinji Ikari felt that he should be giddy. After all, his long lost mother had been abruptly returned to him, an elaborate scheme that would have hurt everyone (but him especially) had been exposed, and the world in general just seemed like a less messed up place than it had yesterday.

Yes, he really should have been thrilled. He should have been skipping through the halls of the base and grinning like an idiot. Instead, he was sitting in one of the corridors, his back propped up against the wall and feeling numb with shock. Indeed, Shinji had felt utterly shell-shocked from the moment he'd found out his mother was alive and had returned, and he had remained so all through the debriefing and beyond. He supposed that was normal enough, but his surprise was slowly starting to erode, and it wasn't euphoria that lay beneath it. It was apprehension.

Somehow, he was certain that it was all going to go wrong. Perhaps something would happen to smash his new chance at happiness, or perhaps his mother would prove to be little better than his father. She had, after all, once condoned the horrible scenario his father and SEELE had hatched.

But she stopped, he thought. She realized it was wrong, and she never did any of those horrible things herself. She just…knew they were happening. Wouldn't it be foolish to hate my own mother for something she doesn't believe in anymore? It's not like I never made a mistake...though none of them were ever quite like that.

Shinji shook his head, which seemed to be filled past capacity with hundreds of thousands of whirling thoughts. It was all just too much, and the future, which should have looked brighter to him, appeared more intimidating than ever.

He didn't know what would happen, but he was afraid to be happy all the same.

Only I could feel like this right now, he thought morosely. I'm so messed up.

He sighed and leaned his head against the wall, closing his eyes.

"Shinji-kun."

Startled, Shinji's head snapped forward and his eyes popped open. His mother was approaching him.

"Oh, Mother!" Shinji greeted her, forcing a smile, and feeling terrible about having to do so.

She was wearing normal clothes, but that amulet was still sitting around her neck, and she was carrying the helmet with her in one hand, almost carelessly. The pieces of gold made it impossible to forget about the fantastic transformation she could undergo.

Yui went down to one knee so that she was roughly eye level with her son, and Shinji suddenly realized that she looked like she was in her twenties. He guessed it was more or less natural that she'd come out of EVA the same age she went in, but it made her look too young to be his mother. It was weird.

"What are you doing here, Shinji-kun?" she asked gently.

"Huh, oh, I…uh…" he stammered, desperately searching for some kind of explanation that wouldn't make him look displeased at her reappearance.

"It's all right, you don't have to tell me," Yui said eventually, then she smiled sadly. "I guess it's going to be a while before we have the kind of relationship that a mother and her son should have."

"Mother…" Shinji spoke, then trailed off, not knowing quite what to say.

"Come on, Shinji-kun," Yui said. "Why don't we go get something to eat and talk for a while? I want to hear all about your life."

"Uh, shouldn't you still be working on figuring out what to do about SEELE?" Shinji asked, then realized that it might sound as if he didn't want to spend time with her.

He shouldn't feel so awkward around his own mother.

"Someone else can do that," Yui said. "You're more important."

Shinji smiled, a genuine smile this time, and got to his feet. Mother and son made their way toward the base's commissary together.

"Dr. Fate was never meant to be just one person," Negal said.

"What do you mean?" Gendo asked.

"Fate was always meant to be two people, a man and a woman, bound together by the power of the helmet," Negal explained. "Only through such a union can Fate ever achieve his true potential. However, the creator of the helm kept this secret, because it would deny him any control over his champion."

"I see," Gendo said, trying to keep his voice level, but the demon could see the light shining in the man's usually cold eyes and could practically hear the wheels turning in his keen mind.

"When two people are united by the power of Fate, all the boundaries between them fall," Negal said. "It is togetherness like no other. If your wife was so bonded with you, it would be impossible for her to not see how brightly your love for her still burns."

"You've captured my interest," Gendo finally admitted. "Now, what is the price for helping me achieve this union?"

"Nothing much," Negal said, fingering the war hammer he held. "The previous Dr. Fate was a powerful enemy of mine. I simply wish for your word that you will never move against me when you're Fate."

"Done," Gendo said.

Negal smiled. "Good," he said. "Oh, one final condition: you cannot allow it to be known that I was the one who aided you. If Fate discovers it was me, and she defeats you…"

"I will not fail," Gendo said.

"Let us hope not," Negal replied.

Blue flames suddenly came into being around Gendo, but they did not burn him. The former commander of NERV closed his eyes and stood still as they enveloped his entire body.

Minutes later, the heavily armored door to his confinement cell was blown off its steel hinges by a blast of demonic flame.

"Well, the food here is every bit as bad as I remembered it," Yui declared as she and her son spoke over a light snack. "I wasn't sure that was even possible."

"Yeah, it's pretty bad," Shinji agreed with a weak smile.

Awkward silence followed. Yui quickly moved to break it. "So, tell me about yourself, Shinji-kun," she said. "I really don't know much about you outside of your role as the Third Child."

"There's really not much else to me," Shinji said bashfully.

"Nonsense," Yui said at once. "How are you doing in school? Do you have any hobbies? Is there a special lady in your life?"

The last question caused Shinji to blush. "M-Mother!" he sputtered.

Yui grinned. "Shinji-kun, I'm your mother. I'm going to be interested in your life, including that part of it," she said. "Especially that part of it. You're just going to have to get used to it."

He sighed ruefully, though part of him had to admit the attention was actually kind of nice, in a weird sort of way. "Uh, I'm doing okay in school," he said, which was perhaps an exaggeration, so he quickly continued, "I play the cello, and no, I don't have a girlfriend."

"I'm surprised," Yui said. "I'd think that a young man as handsome as you would be beating the girls off with a stick."

"Um, can we talk about something else?" Shinji asked, squirming embarrassedly in his seat.

Smiling, Yui relented. "So, you said you played the cello. Did you know that I played, too?"

Shinji nodded. "Yes, in fact, the reason I play is because Uncle gave me your cello and said I should start learning."

"So do you enjoy it?" Yui asked.

"Yeah, I guess so," Shinji said.

"There's something you want to ask me, isn't there?" Yui asked after another moment of silence.

Shinji nodded.

"Go ahead," Yui said. "You deserve to know. Ask."

"Why did you do it?" Shinji asked. "Why did you work on the Instrumentality Project?"

Yui had expected this question, of course, but it still caused her to sigh. "Shinji-kun…I don't know whether you feel the same way or not, but when I was younger, one of the things I wanted most was to make my life count for something," she said. "I wanted to do something big. Something important."

"Okay," Shinji said.

He didn't understand this compulsion; Shinji aspired to not make the world too much worse because he was in it, which seemed difficult enough most of the time. However, he didn't want to divert the conversation away from his mother's narrative, so he didn't tell her this.

"The ideal behind the Instrumentality Project, well, it was about the creation of a whole new world," Yui said. "A world in which famine, disease, war, and death were nonexistent. Where loneliness and pain were nonexistent. Basically, bringing humanity back to Eden by changing all of us, so we'd be happy, safe, and blissfully content for all of eternity."

"It sounds nice," Shinji said quietly.

"Doesn't it?" Yui asked bitterly. "There were signs, even before I was absorbed, that Instrumentality might not be all it was cracked up to be, and the cost of making it happen only seemed to grow and grow. But the idea of making the world a paradise…I was obsessed with it, Shinji-kun. Even more so after you were born. I wanted to make the world perfect for my family. My intentions were good, but that just let me realize how true the old saying about the road to Hell is. I can only hope I can be forgiven for my stupidity."

"Mother, you…I…" Shinji said, but quickly trailed off, not knowing what to say.

The heavy silence came back.

This time Shinji broke it. "Mother, what's going to happen?" he asked. "Not with NERV and SEELE and the world and everything. I mean, with you."

"Well, I guess I'm going to have to find myself a place to live," Yui said, thinking that she did not want to reside within the daunting tower of fate. "I was hoping that you'd come and live with me, though I'd understand if you didn't want to leave Katsuragi. After all, she gave you a home when I couldn't, and your father wouldn't." She added in a sad voice.

"Mother…"

"Don't answer right now, Shinji-kun," Yui said. "Think about it for a while."

He nodded, and the wretched silence returned once more.

"I really did mean what I said before, Shinji-kun," Yui said abruptly. "I really do intend to make things right. I realize this whole thing must come as a shock, and knowing that I was once in on SEELE's plans can't exactly fill you with confidence about me, even knowing why I did it. But please, just give me a chance, like you gave your father one. I promise I won't throw it away like he did."

"I…I think I can do that," Shinji said with a small smile, which Yui returned.

"I'm glad. Maybe by the time I've found myself a place to live, you'll be ready to stay there with me. I'm not sure I'll have time for apartment hunting any time soon," Yui said. "Stopping SEELE is going to take up a lot of my time, and I also want to do some research into healing magic."

"Why?" Shinji asked.

"For your friend, of course," Yui answered.

Shinji blinked. "You think you can fix Toji's injuries?"

"I don't know," Yui admitted. "My predecessor didn't teach me any healing spells, but he was in a rush to give me what I needed to be Fate and pass the mantle. I think it should be possible. Fate is powerful."

Shinji smiled, and for the first time in what felt like a very long time, he believed that everything might turn out all right in the end.

This, of course, was when the alarms went off. Shinji and Yui traded a shocked look, and then quickly got up and began to run toward the command center.

"What's going on?" Yui asked as she and Shinji emerged onto the middle tier of the base's nerve center a few minutes later.

"The base seems to be under attack," a chagrined looking Fuyutski answered.

"Is SEELE making a move already?" Yui asked incredulously.

The men of that secret cabal were dangerous, no doubt, but she hadn't believed for a moment that they could react so quickly to the abrupt power shift within NERV, assuming they'd even learned of it yet.

"No, though I almost wish it was them," Misato answered. "They're coming from inside the base, and it looks like they breached the Commander's cell."

"Who are they?" Yui asked.

Rather than answer, Misato looked down at Aoba. "They're destroying the security cameras—and probably everything else—in their path, but I'll see if I can get a shot from one that's still working," the tech said, typing furiously at his keyboard as he did so.

A window soon popped up on the main screen showing one of the corridors that was under siege, and Yui's eyes widened as she saw it. The enemies who had invaded NERV were not human in nature, nor where they Angelic.

The screen showed a number of four legged beasts running through the halls of the base. They were vaguely dog-shaped, but no one would ever mistake them for man's best friend. Each one had bluish, leathery skin, misshapen heads, a pair of long horns, and far more teeth and claws than seemed necessary.

"Kent wasn't kidding about having to stop demons and things all the time," Yui said to herself, then turned her attention to Misato. "I'll take care of this. Stopping those things isn't a task for NERV security."

The Operations Director had expected as much, and had already evacuated the areas that the demons were tearing up.

"Good luck," she said.

"Be…be careful, Mother," Shinji said.

Yui smiled, and then again donned her golden helm.

Minutes later, Dr. Fate raced downwards through the corridors of NERV headquarters, her feet not even touching the floor as she went. She told herself that she was moving with such haste because the people who worked for the organization were all in great danger so long as demons were allowed to run free within the base, but that was only part of the reason.

In the face of all logic and everything her head was telling her, she was worried about Gendo. She would never forgive the man for what he'd done to their son, and perhaps it was just the good memories they'd had together influencing her, but she had no desire to see him torn to bits by otherworldly monsters, at least not after he'd already been defeated and rendered harmless.

She heard the growling on the demons before she saw them and slowed her pace, not wishing to rush right into an ambush. Peering carefully around a corner, Fate winced as she saw a pack of the demons tearing apart the remains of what had once been a NERV security guard.

"Infernal beasts!" she shouted as she showed herself. "You have no place on this world!"

The demons immediately left their old prey behind and started growling at her, each of them frothing at the mouth like a rabid dog. As one, they pounced at her, teeth and claws flashing under the hallway's bright fluorescent lights.

"Jaduan shield!" Fate shouted.

A barrier of golden light formed in front of her, and the demons crashed into it rather than her, then went falling to the floor, growling and glaring at her hatefully.

"You will return to whatever pit of a realm you crawled out of!" the sorceress yelled, yellow light appearing around her hands. "So Fate commands!"

Golden radiance enveloped the demons, all of which released cries of pain, and then their bodies appeared to disintegrate as they were banished back to their home realm. Fate put her hands down and nodded in satisfaction.

Yet before she could continue on, more growls sounded, and Fate looked around to see that more of the vaguely canine demons were approaching her from either end of the corridor.

"You dare challenge Fate?" she snapped. "Be gone, all of you!"

Blasts of magical energy burst from both of her hands, one going down either end of the hallway and incinerating every demonic beast in its path.

"Are there any others here who wish to test the power of Fate?" the sorceress demanded. "If so, step forward!"

At first, only silence greeted her. Fate was about to move on when she heard the sound of heavy footfalls. Another demon, this one similar to the others but the size of horse, emerged from around a corner, and upon its back rode—

"Gendo?!" Fate exclaimed, her eyes widening.

The former commander of NERV was clad in a black outfit, over which was a chain mail vest made from some blue metal. The orange lenses of his glasses had been replaced with black ones, and he held a war hammer that appeared to be made of bone in one hand.

"Hello, Yui-chan," he greeted her in a serious tone.

She considered reminding him again that he no longer had any right to call her "-chan" but quickly discarded the idea. There were more important issues to be addressed.

"What have you done, Rokubungi?" she demanded.

The sound of his old surname caused Gendo to sigh in a long suffering sort of way. "I'm only doing what I need to do to make you come to your senses, Yui-chan," he said.

"You want to make me to come to my senses?" Fate demanded. "You're the one who's deluded, Rokubungi!"

"Are you sure?" Gendo asked. "Listen to yourself, Yui. You sound nothing like yourself. That helmet has changed you."

"Perhaps I behave a little differently while I wear it," Fate conceded, "But I'm still me beneath it. You're nothing like the man I once knew. Now surrender. If you make me fight you, I won't hold back."

"I'm sorry, Yui-chan, but I can't do that," Gendo said.

With that, he raised the hammer he held. Blue flames burst into being around the head of the deadly weapon and shot out toward Fate. The sorceress was so shocked that her husband was actually attacking her that she was barely able to conjure a barrier to block the strike in time, and the force of the blow sent her staggering.

Before she could regain her equilibrium, tendrils made from some kind of black sludge burst out of a nearby ventilation grate. Fate let out a gasp and tried to dodge, but they were far too quick, and wrapped themselves around her wrists and ankles.

"Whatever you are, release me, now!" Fate shouted as she struggled against her bonds.

"I don't think liquefied human misery responds to threats, Yui-chan," Gendo said as he dismounted from his demonic steed. "I don't remember you ever being so loud and angry. Fate's influence must havechanged you even more than I'd believed."

"What are you doing?" Fate demanded as Gendo approached her.

"Making things right," Gendo answered, grabbing hold of the amulet of Anubis around her neck.

"No!" Fate shouted. "Don't do—"

Gendo pulled the amulet up over her head, and Fate immediately went limp in the black tendrils' clutches, the better part of her soul now separate from her body.

"Don't worry, Yui-chan," Gendo said as he placed the amulet around his own neck. "Soon we'll be together again. Soon, you'll understand everything."

With that, he grabbed the golden helmet on Fate's head and easily removed it. Gendo took a deep breath and whispered, "I love you, Yui-chan."

Then he jammed the helmet over his own head.

The effects were instantaneous. The sound of screams from two different people—one male and one female—erupted from within the helm, while golden light shot forth from the bottom and the eyeholes of the powerful relic, as though a minuature sun was housed within it.

Gendo went staggering and quickly fell to the floor, where he lay motionless.

Meanwhile, on the command center, a heavy silence fell. Everyone had been watching Dr. Fate do her thing via one of the few intact security cameras in the area, and it had seemed like it was just a matter of time until NERV was demon-free.

That was, until Gendo had made his appearance.

"I don't know anything about magic," Misato said as she looked at the motionless forms of Yui and Gendo on the main screen, "but I'd say that isn't good."

"I'd say you're right," Maya agreed in a grim tone.

"Then it looks like there's only one thing to do," the Operations Director said. "I want a squad of our security forces assembled on the double. We'll have to repel this attack ourselves."

"Should I tell them to make sure they're carrying their silver bullets?" Aoba asked sarcastically.

Misato glared at the long haired tech. "No. Tell them to get the biggest guns from the armory that they can find."

"Yes, ma'am."

"Uh, Major?" Makoto spoke up. "Did you send Shinji somewhere?"

"What?" Misato said, turning her head this way and that as she searched for her charge, only to fail to locate him.

He wasn't on the command center anymore, though she was sure he had been a minute ago. She'd seen him there right before Dr. Fate had started to tangle with Gendo.

This, of course, added up to one inescapable, and very unpleasant, conclusion.

"Shinji's going there!" Misato exclaimed, pointing at the image of Gendo and Yui's unconscious forms on the main screen. "Find him, and send security to stop him!"

"It's going to be difficult to locate him," Makoto said, even as he began to type furiously at his keyboard. "Most of the surveillance in that part of the base—"

"I'm not interested in excuses," Misato snapped. "Just do it!"

Shinji Ikari knew he was crazy. There was really no other way to describe someone who lacked any supernatural abilities whatsoever but was rushing to the scene of a potentially deadly paranormal conflict anyway.

In a way, he was pleased with the way he'd been gripped by madness. It seemed that these moments of insanity were the only times when he really managed to accomplish things, like slaying the Fourth Angel or diving into a volcano to rescue Asuka.

Maybe it's just left over craziness from trying to fight the Angel earlier, he thought wryly as he continued sprinting down flights of stairs.

Of course, Shinji knew that there was more to it than that. It seemed like he might have finally been given what he'd wanted all his life: someone who cared about him unconditionally, just because he was her son. He wasn't letting someone take that from him, not after mere hours.

Even if he wasn't entirely ready to believe that he truly had it.

After a few minutes of running, Shinji came to the part of the base where the demons had been let loose. Everything was utterly trashed, and the bodies of the NERV personnel unfortunate enough to have been in the area at the time littered the floor, all of them savagely torn apart.

Looking at them, Shinji felt the urge to vomit and clamped his throat shut. He fervently hoped that the demons weren't around any longer, now that his father was incapacitated.

This is so nuts, he thought to himself.

The sound of running footsteps suddenly reached his ears, and moments later, a voice rang out. "Pilot Ikari! You are ordered to return to the command center! We're here to escort you there!"

Damn, Shinji thought, detouring down another hallway to avoid the men.

Fortunately for him, the layout of NERV headquarters wasn't actually that confusing in this area, since there was little variance from floor to floor. That he had a pretty decent sense of direction also didn't hurt his ability to take an alternate route without getting lost, either.

I hope they don't hear me, Shinji thought, trying and failing to stop panting for breath for a moment, to no effect. His lungs burned, but the air inside them felt almost frigid. I really need to workout more often.

The security personnel searching for him were making too much noise themselves to hear the Third Child's panting, and soon Shinji had put some distance between himself and them. He wasn't going to get dragged back up to the command center. In the back of his mind, he wondered if that was really a good thing.

After traversing down a few more floors, Shinji finally reached the place where his parents lay. The large demon his father had been using as a mount stood there, but it made no move to attack Shinji. He gave it a wide berth all the same as he approached Yui and Gendo.

Once right next to them, he squatted down slightly, propping his hands on his thighs and panting.

Okay, I'm here, so now what? He wondered.

"Damn you, Rokubungi."

Shinji's head snapped up. That had been his mother's voice, but she looked as still as she had when he'd arrived; she could have been in a coma for what anyone could tell by looking at her. It was a disturbing sight.

"Yui-chan, I'm doing this for us."

That had been his father's voice, and it had come from Gendo's prone form on the floor. Shinji looked down and him, frowning.

"You're doing this for you!"

That had been his mother's voice again, but it had come from beneath the golden helmet that Gendo currently wore.

What the hell? Shinji thought, tilting his head as he looked down at his father. They're…they're both inside him. But how? And why?

The second question was a riddle he didn't think he'd ever be able to answer, not if he was given a thousand years to ponder it. However, the question of how his father had done this was another matter. The man was wearing the golden helmet his mother used to change into Fate, and he also noticed that the amulet—the one piece of Fate's costume that Yui wore even when she being herself—was around his father's neck.

Shinji kneeled down and took the amulet in one hand, suddenly knowing what he needed to do. He pulled the thing up off of Gendo's head, then placed it around his own neck. Next, he took the helmet off his father.

"This is probably the worst idea I've ever had," Shinji decided with a sigh, just before he donned the helmet.

The result of this was exactly the same as when Gendo had done it. Golden light exploded from within the helmet, Shinji screamed, and then he went collapsing down to the floor.

Some indeterminate period of time later, Shinji awoke with a groan and slowly sat up.

"What happened?" he muttered to no one in particular, his mind fuzzy.

He reached up to rub his head, and as his fingers made contact with his hair, Shinji suddenly remembered that he was supposed to be wearing headgear at the moment.

The realization caused him to abruptly waken fully, and he looked about wildly, gasping as he took in his surroundings. He was sitting on a tiny island of gray, barren rock, but his perch wasn't surrounded by water. Instead, it floated in an endless expanse of black, star-filled sky.

Shinji's hands reflexively went down to the ground and his fingers dug into the dirt beneath him, as though he was trying to grip it so as to keep himself from floating away into space.

Where am I? He wondered, his head swimming. The amulet? The helmet? Does it matter?

He decided that it probably did, but that he probably would never be able to figure it out.

"Why do you resist this union, Yui-chan? Everything will be all right, if you simply allow yourself to become one with me."

"You're a monster! I don't want to be with you ever again!"

Shinji looked up to where the voice had come from, and soon spotted his mother and father. They were on a large stone island some distance away from where Shinji found himself. Yui was dressed in the garments of Dr. Fate, save for the helmet, which was conspicuously absent. Gendo was still dressed in the bizarre outfit he'd been wearing before. As Shinji watched, azure flames burst forth from the head of Gendo's bone war hammer and went streaking toward Yui, who quickly erected a shield of golden energy to defend herself.

"I have to get over there," Shinji muttered to himself. "But how?"

Seeming to respond to his desires, a number of the floating islands of rock around his began to move, quickly forming a series of stepping stones that led from where he was to where his parents were.

"Cool," Shinji said. "Kind of creepy, but cool."

Doing his best not to look down, Shinji began to jump from island to island, moving as quickly as he dared. He didn't know for sure what would happen if he were to fall into the endless abyss below him, but he wasn't feeling much need to experiment.

Finally, after a short but rather harrowing journey, Shinji had reached the island upon which his parents fought one another. It was easily the largest landmass in the surreal place in which he'd found himself, even boasting a small mountain in the center, though it was as barren of vegetation as all the others.

Yui and Gendo failed to notice him at first, and he watched as his father sent another plume of blue flame spiraling toward his recently returned mother. She again blocked it with her magic, but he heard her grunt with exertion and feared that she was weakening under the constant, fiery assault.

Shinji began to creep closer to the scene of the battle, using spikes of rock for cover to prevent himself from being seen.

"Everything can fine again, Yui-chan," Gendo said, brandishing his war hammer. "Things can be the way they used to be again. We can be happy again!"

There a distinct note of madness in his father's voice, and Shinji suddenly realized that the man was changed. Something within him had broken or snapped that day, and the icy cold manipulator was gone, at least for the moment, and a different but no less dangerous figure stood in his place.

"Things can never be the way they used to be, Rokubungi," Yui told her husband.

"Yes, they can!" Gendo shouted, and to Shinji he sounded quite mad. "All you need to do…is submit!"

Flames burst into being around the head of his war hammer again, and Shinji was in motion before he realized that he'd decided to do something.

"Father, stop!" Shinji shouted, emerging from his hiding place and grabbing hold of the war hammer's shaft. "You can't do this!"

"You?" Gendo said, his usually impassive face the picture of shock. Then his features rearranged themselves into an expression of contempt. "I don't know how you got here, but you have no business in this place. Leave. Now."

Shinji shivered, realizing abruptly that he couldn't just see and hear his father's obvious disdain for him, he could actually feel it, like cold fingers reaching into his chest and touching his heart. Apparently, the walls between people were a little less sound in this strange nether place.

Yet he didn't release his hold on his father's weapon. "I won't run away," he said softly.

"Fine," Gendo growled.

With a savage jerk, the former Commander of NERV pulled his war hammer from Shinji's grasp, causing the Third Child to fall to the ground, landing painfully on his rear.

"If you don't have the sense to leave," Gendo said, raising the hammer, "I will force you to leave!"

"Don't you dare try to hurt my son!" Yui screamed as Gendo swung.

Two things happened simultaneously. First, a sphere of golden light formed around Shinji, and Gendo's hammer fell upon it without so much as scratching the magical barrier.

Second, Shinji felt another wave of emotion that was not his sweep over him. It was rage of such intensity that it shocked him, and it was primal, almost feral even. It was the anger of a mother who was seeing her child's life threatened, and the overwhelming need to protect that child. Shinji had felt the like of it only a few times before.

When Evangelion Unit One went berserk.

Even after he'd realized that some piece of his mother was inside the purple and green destroyer, he had always believed that some of that irresistible tidal wave of emotion he'd felt coming from the machine those few times it had gone ballistic had been partially that of the Evangelion itself. That the violent, perpetually angry nature of the beast had contributed to the pure rage that had been unleashed on his behalf.

Now he knew that wasn't true. The need to protect him, the molten fury at those who would hurt him…that had all been from his mother.

And as terrible a time as it was for it, Shinji felt a lump forming in throat at the knowledge that anyone could get so enraged over someone threatening him, and would be willing to do anything to see him continue to live.

Mother…

Suddenly, Shinji was cruelly brought back to reality as Gendo capitalized on the interruption in the battle. Conjuring such a powerful shield for her son had left Yui winded, and when Gendo sent another ball of fire flying her way, she wasn't able to defend herself.

"Argh!" she cried in pain as she was knocked down to the ground, the front of her costume scorched black by the heat.

"No!" Shinji screamed, rushing over to her and kneeling next to her supine form.

He was supremely relieved when he found she was still breathing.

"Get away from her, Shinji."

The Third Child looked up to see his father slowly approaching, and he scowled. "Not on your life."

He wouldn't allow his mother to be taken from him again, and he'd be damned if he allowed his own interference in the battle to help his father claim victory. He wasn't going to let himself screw this situation up.

"You don't understand what I'm trying to do," Gendo said, again sounding almost like the shrewd calculating man Shinji knew. "All I want is to make your mother understand me again. Once I achieve that, she and I can be together again, and our family can be whole again. Don't you want that?"

"I don't want you in my life," Shinji said flatly. "Not anymore."

Gendo's features hardened. "I haven't come so close to my goal to be stopped by the likes of you. Step aside, or I'll kill you," he said bluntly.

"No, go away!" Shinji yelled.

"Move aside or die," Gendo hissed, taking another step forward.

"I said go away!" Shinji shrieked.

And then something that shocked both father and son happened. Orange light flared into existence between them, forming into a hexagonal barrier. This brilliant wall of force slammed into Gendo, sending him flying. The man screamed as he sailed through the air, until he crashed into the side of mountain, groaning.

"H-How did I do that?" Shinji stammered.

"AT Field," Yui groaned.

"Mother!" Shinji gasped, turning to her. "Are you all right?"

"I'm about as all right as can be expected," Yui winced as she sat up. "To answer your other question, the power of the human AT field is paradoxically both weaker and stronger in this place. Gendo hoped to capitalize on that weakness by merging with me and taking control of Fate. It looks like your experience manipulating AT Fields in EVA allows you to utilize the strength of them in this place."

Shinji nodded. "Mother, is it over? Did we win?"

She shook her head gravelly. "No. Your father will draw more power from his demonic ally and come at us again."

"Then what do we do?" he asked.

Yui hesitated for a moment, and when next she spoke, it was with reluctance. "I know a spell that should sever Gendo's tie to his new friend, but I need a few moments to prepare it. Longer than we have," she said. "Shinji-kun, I hate to ask this of you, but do you think you can keep him occupied for just a little while?"

Rather than say anything, Shinji just nodded.

Mostly because he was afraid that he'd show how frightened he was if he opened his mouth.

"You're braver than you give yourself credit for, Shinji-kun," Yui said warmly. "I'm proud of you. Now go. Hopefully, this won't take too long."

He nodded and headed away from his mother, toward the mountain in the center of the island. From the corner of his eye, he could see Yui taking cover behind an outcropping of rocks, hiding herself from view.

For a moment, his father didn't move from the place where he'd fallen, and Shinji dared to hope that he'd remain there until his mother was ready to make her move.

However, he had no such luck. The man abruptly got to his feet, a halo of blue flame surrounding him now, and a pair of black bat wings burst from his back, tearing through both his shirt and his chain mail armor as though they were made of paper. He looked about, and Shinji could see a wicked red light emanating from behind the black lenses of the glasses he wore.

When he locked that burning gaze upon his son, it was all Shinji could do not to quail in terror.

"Where is she?" Gendo demanded.

Shinji gathered up every ounce of courage he possessed and shouted back. "If you want her, you'll have to go through me first!"

Without another word, Gendo spread his new wings and went soaring toward Shinji, leaving a trail of ash and embers as he went.

The Third Child took a deep breath as he watched this terrible parody of a human being streak toward him, and he did he best to picture the indestructible barrier of orange light.

"AT Field full power," he said softly.

Dust and small rocks were kicked up in a rapidly expanding circle around the Third Child by the power of the forces he was invoking. It looked like a subtle display of awesome power, and Shinji only hoped that it would be enough.

Gendo lashed out with his war hammer, and the shield of orange light flashed into being as the hammerhead slammed into it.

The force of the blow, which Shinji felt like it was a pressure on his mind, was incredible, but it nearly paled next to the force of his father's emotions, which Shinji could once again sense.

At that moment, Gendo Ikari hated Shinji Ikari with every fiber of his being, just like he hated everyone who tried to prevent him from regaining Yui. The intensity of his hate, which had been mere contempt only minutes earlier, was staggering.

Yet, it allowed Shinji to discover a simple and wondrous thing.

He didn't care that his father hated him then. He didn't care what his father felt at all.

Despite Gendo's awesome demonic powers, his ability to hurt his son had never been more diminished.

"You won't win!" Shinji shouted. "I won't let you!"

"You can't stand in my way forever," Gendo retorted through clenched teeth.

Shinji didn't bother to reply, doing everything he could to maintain his AT Field. It was tremendously powerful, but his father's assault was as well.

Immovable object against unstoppable force. It's the Tenth Angel all over again, he thought grimly, trying not to recall how close he'd come to losing that battle. If Rei and Asuka had shown up any later than they had, he would have buckled beneath the kamikaze Angel's weight.

"Rokubungi!"

"Yui-chan!" Gendo exclaimed, immediately leaving his son and flying toward her.

No longer needing to defend himself against his father, Shinji allowed himself to collapse to the ground, feeling exhausted.

"By the eye of Ra, with the symbol of everlasting life, I sever your connection to the being from the pit, Rokubungi!" Yui shouted.

A large ankh the color of molten gold came into being around Gendo, and the demonically empowered man was suddenly attached to the symbol. He let out a scream of agony as the light pulsed and then flared, momentarily blinding both Shinji and Yui.

When mother and son could see again, Gendo lay on the ground, unmoving and looking quite human again.

"Is it over?" Shinji asked, fearing to hope that this hellish experience had finally come to a close.

"Yes," Yui said with a tired nod. "It's really—"

"Just beginning."

A ball of azure flame suddenly burst into life where Gendo lay and quickly expanded, sweeping into the two who stood next to him. Shinji and Yui cried out as they were both thrown backwards by the force of explosion.

"Not bad, Yui-chan," Gendo said as he got to his feet and dusted himself off, his demonic features having returned. "However, that spell's a little outdated. Probably from the previous age."

Yui's eyes narrowed, and it was clear that she had little tolerance remaining for this battle. "Gendo, enough!" she shouted as she sent a bolt of magical energy his way.

The bearded man easily deflected the attack with his hammer. "It's never enough! Not until I have you back!"

He swung his hammer then, aiming right for Yui. Shinji was by his mother's side in an instant, summoning an AT Field into being.

"Father, stop this!" Shinji begged as the man furiously assaulted the shield of orange light.

"No!" Gendo yelled. "I won't! I won't!"

"But don't you realize what you're doing?! You're going to destroy everything you ever wanted!" Shinji yelled.

The words had come out of his mouth before they'd run through his mind, but Shinji immediately realized they were true, the same way he'd realized that his father had hated him earlier, and that his mother loved him with all her heart.

Not only that, but to Shinji's immense surprise, he also realized that his mother wasn't the only person included in the category of "everything Gendo Ikari had ever wanted."

She was the one he wanted most, to be sure; she was paramount to Gendo. But if he possessed the power to make the world exactly as he willed it, that world would include Shinji Ikari. Gendo had cared about him once, but he'd pushed his son away, or more accurately, run away from him, because—

Shinji's eyes widened, and he barely noticed when Gendo's attacked relented.

"What did you say?" the man whispered.

Forcing himself back to the present, Shinji turned to look at his father. "Look, influenced by her new powers or not, Mother's never going to want to be with you again," he said, concealing the rioting emotions inside him as best he could. "And even I can't forgive you for the things you've done. You're never going to have your happy little family back. We'll fight you until our real bodies wither and die before we take you back. Even if you win, the closest you'll get is some…some pale shadow of a family where you force Mother and maybe me to be around you. So if you ever truly cared about us, then think about us before what you want and stop this."

"I…" Gendo stammered.

"Father?" Shinji asked.

"I…" Gendo sighed. "I can't."

He swung his war hammer again, but before it could make contact with Shinji's AT Field, golden light flared around Gendo once more, and this time four ankhs came into being around him.

"I see how my previous spell was obsolete," Yui said. "You always did say I was a fast learner, Gendo. Guess you were right."

He screamed, and the ankhs abruptly winked out. Gendo collapsed, and this time he did not get up.

"Now is it over?" Shinji asked wearily.

"Yes," Yui said. "Now it's over."

"Hey, look, he's moving! Shinji's moving!" Misato exclaimed.

Asuka and Rei turned and saw that the Third Child was indeed stirring for the first time since he and the other two Ikari's had been brought to NERV Medical. Moments later, Shinji released a groan and sat up, removing the helmet from his head.

"Ugh," he said. "Where am I?"

"The ward, baka," Asuka said. "I hope you realize that what you did was friggen' insane."

"Yup," Shinji replied with uncharacteristic nonchalance. "What happened to all the demons that were attacking?"

"They disappeared a little while after you put that helmet on," Misato answered. "Just up and vanished into thin air."

"Are you well?" Rei asked him softly. "What happened to the Commander and Mrs. Ikari?"

At the mention of Gendo, blue light suddenly arced out of the amulet that was still around Shinji's neck and went straight into his father's body, which lay on the bed next to his own. Gendo released a gasp, opened his eyes, and tried to sit up. However, this last action was prevented by the fact that his wrists were handcuffed to the bed's metal headboard, along with his ankles.

"He'll live," Shinji said.

With that, he got out of bed and removed the amulet, then placed it around his mother's neck. Yui sucked in a gasp of air and sat up.

"Oh," she groaned, rubbing her eyes. "I do not want to do that again anytime soon."

"No argument here," Shinji agreed.

"Where's Gendo?" Yui asked.

"Right there," Shinji said, gesturing at his father's bound form.

Yui's brow drew down in a deep frown as she approached her husband, taking her helmet from her son as she went.

"Major Katsuragi," Yui said, not turning her angry glare away from Gendo. "Gendo Ikari died during his foolish attempt to escape, understood?"

"Wait," Misato said, "what are you going to do?"

Yui placed the golden helm over her head, transforming once again into Dr. Fate. "After today, I don't trust any prison constructed and guarded by normal men and women to hold him. I intend to incarcerate him myself, in a place he will never escape from."

Misato hesitated for a moment, then nodded. "All right," she said. "The records will show Gendo Ikari died during his escape attempt."

"Thank you, Major," Fate said, then turned her attention back to the former commander. "Come along, Gendo."

An ankh shaped portal appeared in the room, blinding the occupants with its light. When it had faded, Fate and Gendo were nowhere to be found.

"Where did she take him?" Asuka asked.

"I'm not sure we really want to know," Shinji replied.

"Where are we?" Gendo asked as he looked around the stone structure they had appeared in, with its dizzying and impossible staircases going off in all directions.

"My tower," Fate answered. "In this place, not even the most powerful demon will be able to come to your aid."

"Yui-chan…"

"I told you, don't '-chan' me," Fate said in a dangerously soft voice.

Suddenly, four chains, each one attached to the walls, magically sprang to life and moved toward Gendo. The bearded man gasped as each chain wrapped itself around one of his legs or arms, drawing tighter and tighter around him until he was suspended in the air by the links of metal in a spread eagle position.

"Yui…" Gendo said, his voice pleading.

"You know, Gendo," Fate said, "part of me, a very small part of me, thought that you weren't entirely beyond redemption. I believed that one day, you might have been punished enough, that would come to realize how horrible you'd been since I was absorbed into EVA, and that you could change for the better as a result of it. I guess it just goes to show that I can still be as foolish as I was before I was absorbed into EVA, since what you did today certainly proved me wrong."

"Yui, please…" Gendo begged.

"Can you believe that for a moment, I actually thought I might want you back someday?" Yui lied, twisting the knife.

"What?" Gendo gasped.

"The magic in this place will sustain you for the rest of your natural existance," Fate said, another ankh shaped portal opening behind her. "Good-bye, Gendo. Have a nice life."

"No!" Gendo shouted. "Please, don't leave me, Yui! Not again!"

Fate silently walked through the portal, which vanished after her.

Later that evening found Shinji, Asuka, Misato, and Yui at the Katsuragi apartment. Misato had generously offered Yui the use of her couch until she could find a new home, and Yui had quickly accepted.

Misato had also declared that a party was in order, to celebrate the events of the day, despite how exhausted her roommates were from the battles they'd waged mere hours earlier. Fortunately, said party had consisted of Misato ordering take out food and then her drinking far too many cans of Yebisu, so it really wasn't very much different from a normal night there.

You'd think someone like Misato would be able to throw a more exciting party, Shinji thought with little real mirth as he sat on the apartment's balcony and looked up at the night sky.

He heard the sound of the door between the balcony and the apartment sliding open, and Yui walked up to him. "Mind if I join you out here?" she asked.

"Of course not," Shinji replied, and Yui sat down in one of the other deck chairs present.

"You know, Shinji-kun, Misato mentioned to me that this building is mostly empty," she said. "I could probably get one of the apartments next to this one without much trouble."

"I'd like that," Shinji said. "It would be almost like not moving away from here at all."

"So you'll come and live with me?" Yui asked hopefully.

Shinji nodded. "Yeah, I decided that I want to."

It would still be a while before they had the kind of relationship a mother and son should. Their time in that strange realm where he could practically read the minds of his parents hadn't changed that. Now, however, he was certain that they would have that relationship eventually, if they were willing to work at it.

"I'm glad," Yui said.

He gave her a small smile and nodded.

"You've been very quiet since we escaped Gendo," Yui commented. "Any particular reason for it?"

Shinji hesitated, briefly considering telling her it was nothing. Then he disregarded the idea.

"When we were there…wherever there was, I could sort of sense you and Father," Shinji said. "Almost see what you were thinking at times."

Yui nodded. "I could, too. It was an effect of the AT Fields being weak there."

"Well, when I was fighting with Father, I saw that he had cared about me at one time," he said.

"Of course he did," Yui said. "You're our son."

"But after you died, he sent me away," Shinji said. "I always thought it was because he didn't care about me anymore, or even that he never had, but that wasn't it. He sent me away because he was afraid that without you around…he'd only hurt me."

"I can't believe he didn't realize how absurd that was," Yui said.

"I can," Shinji said, his eyes showing a haunted expression. "Mother, just before you came here, I was leaving the city. I was going to leave forever…because it seemed like I only hurt the people I care about when I'm around them."

"Shinji-kun—"

"Don't you see?" he asked, looking pale. "I'm just like him."

"Shinji-kun, listen to me," Yui said firmly, and he nodded and looked at her silently. "Look, Gendo's blood runs in your veins. As much as you don't want to see any similarities between the two of you, there will be a few. But your genes don't dictate everything about who you are; it's not like you have no say in it. You know firsthand how much it hurts when someone you care about pushes you away, regardless of whether or not they're doing it out of some sense of keeping you from harm. Learn from your father's mistake, and you won't be like him. Understand?"

"I think I do," Shinji nodded.

"Good," Yui said. "You know, Shinji-kun, you handled yourself very well today. I think most people in your position would have been so stunned and confused by all the magic that they wouldn't have been able to do anything."

"Oh, it wasn't that big of a deal, really," he said modestly.

"You're being too humble, Shinji-kun," Yui said. "You're very talented. Who knows, maybe when it comes time for me to stop being Dr. Fate, I can pass the helmet to you."

"R-Really?" Shinji asked, shocked.

"It's certainly possible," Yui replied with a smile. "Now I suggest you get to bed, young man. You've had a very long day, and you need your rest."

Shinji smiled. "Yes, Mother."

He kept smiling as made his way to his room, dressed for bed, and lay down. There were a number of trials that still awaited them all, not the least of which were the remaining Angels and whatever SEELE would throw at them. However, with his mother returned to him and the power of Fate on their side, he was confident they could pull through.

For the first time in his life, he was optimistic about the future.

Author's Notes: And so ends Yui's SOE2 fic. I don't really have a whole lot to say here. All in all, I think this one came out pretty well.

Most of my reviewers asked about the lack of any real focus on Shinji's reaction to Yui's return in part one. It was a legitimate thing to bring up, and if I had to write this over again, I'd probably include that in part one. At the time, however, I figured that Shinji would probably be too shell-shocked to be feeling much of anything yet, and since I knew part two would feature him heavily, I decided to leave him mostly out of part one.

Anyway, thanks as always to my readers and reviewers, and thanks to my beta reader as well.

Omakes

Ill Thought Out Prison

"YUI! COME BACK YUI!" Gendo screamed at the top of his lungs.

His words echoed through the numerous corridors, stairwells, and passageways in the tower of fate, but no one answered him. He was alone in great stone structure, as he had been for hours upon hours now.

"Yui! Yui! Let me go!" Gendo cried, pulling uselessly at the chains which kept him suspended in the air. "I'll do anything! Anything!"

If someone who knew Gendo could look upon him now, they'd assume that he was a broken man who was giving voice to the pain from Yui's rejection, as well as having had all his plans reduced to ash.

That someone would be wrong; Gendo had passed that phase hours ago.

"PLEASE, YUI!" he sobbed. "I JUST WANT TO GO TO THE BATHROOM!"