Disclaimer: I do not own Naruto or Mega Man Zero.

Foreword: Naruto is one of my favorite male manga characters, mainly for his backstory and his potential for growth while Ciel is one of my favorite female video game/manga (yes, there is a manga…although it's pretty bad) characters, mainly for her character design. I figured I'd try a Mega Man Zero and Naruto crossover. To my knowledge, there isn't a single one yet.

This setting of the story is mostly the setting used in the Mega Man Zero games. However, for storytelling purposes, I will make changes as I see fit.

Electronic Diary Entry #2-1031-1

"It was the best of times, it was the worst of times, it was the age of wisdom, it was the age of foolishness, it was the epoch of belief, it was the epoch of incredulity, it was the season of Light, it was the season of Darkness, it was the spring of hope, it was the winter of despair, we had everything before us, we had nothing before us, we were all going direct to Heaven, we were all going direct the other way…"

…and no other words could better describe this era.

Humans lived in a utopia called Neo Arcadia. "Heaven on Earth," it was called, and unsurprisingly so. Humans were free from labor, worry, and sorrow. Even death was held at bay with incredibly advanced medical technology, allowing humans to live double or even triple their normal lifespans.

Yet…

It was a perfect world built upon the remains of innocent Reploids. After the Elf Wars, there was peace, but also a grave energy shortage. Copy X, the de facto ruler of Neo Arcadia, decided to prioritize human quality of life and ordered the retirement of countless Reploids in an effort to save energy.

I could not sit and watch. It was my responsibility. After all, I…I was the one who created Copy X. I fled Neo Arcadia and created the Resistance as a haven for Reploids who had been falsely condemned by Neo Arcadia.

But there was little hope. Copy X was every bit as strong as the original, legendary X.

And so, I headed towards the legendary ruins together with the Reploids that were being pursued by Neo Arcadia.

Yes…towards the ruins where our one hope remained…

~ Ciel

(adapted from Ciel's Memories: Prologue – Mega Man Zero Audio Drama)

"Hu…huff…huh…huff…" Ciel panted as she ran as hard as she could along the corridors of the abandoned shrine.

Ciel was an "Enlightened One," a human with a modified genome. Relative to normal humans she had higher intellect and stamina, allowing her to work more effectively and for longer hours.

But that didn't mean that she could outrun combat Reploids indefinitely. No matter how much human DNA was optimized, humans could never match the potential of Reploids.

"Ciel, this way! Quickly!"

Ciel quickly jumped to the side to join Milan and several other Resistance Reploids. They all held their breaths as Pantheons and Golems passed their hiding spot.

They were currently on a mission deep inside Neo Arcadia to find the legendary Reploid Zero. They had studied the legends and concluded that Zero was sealed in a large underground laboratory the size of a small city. They had found the city, but so had Neo Arcadia.

And thus, Neo Arcadia was doing everything in its power to prevent the Resistance from getting their hands on a powerful warrior.

It was a race in which the Resistance had a head start in but the Neo Arcadians had finally caught up. And considering Neo Arcadia's brutality towards any dissenters, that wasn't a good thing for them.

"Th…thank y…you," she gasped out. "I'm sorry that I'm slowing all of you down."

"No," Milan shook his head. "You're the one who gave us purpose and even a chance to survive. You're the one who even found out about Zero. We would never think that you were slowing us down."

"I sense it," a voice interrupted in an earnest tone. "Follow me."

They all looked up to the Cyber-Elf who had spoken. Passy, Ciel's Cyber-Elf friend, had her eyes closed in an effort to sense the ancient power around them.

"Let's go," Ciel whispered to her friends and subordinates before they followed Passy.

Soon, they came upon a large circular room that had fallen into ruin. Even compared to the rest of the abandoned shrine, this room seemed to be in especially poor condition. In spite of that, however, Ciel and the other Resistance members could tell from the marks on the double doors that this room was special.

"A dead end?" Ciel lamented in frustration when she pushed futilely against the doors.

It was so unfair!

They had come so far to fail at the very last moment. There had to be something beyond the doors. They absolutely had to find a way to open the doors!

"No. I feel strong energy emanating from here. This must be the place," Passy remarked as she flitted side to side around the doors. "We just need to open the doors with sufficient amount of force."

Ciel watched appraisingly as Milan stepped up and pounded on the thick stone doors.

"The doors are surprisingly sturdy," Milan said with a frown. "There doesn't seem to be anything in particular protecting the doors so I think we can destroy them with our busters, but that will alert every Pantheon in the area."

There was a pause. With only a dozen Resistance soldiers, they had no chance against the hundreds of Pantheons scourging the area. The Resistance "soldiers" were actually civilian Reploids volunteers who had very little combat ability or training. They would be hard pressed to fight even against an equal number of Pantheons.

Against hundreds? It was definitely suicide.

Ciel opened her mouth, but Sourde, a stocky Reploid, put up his buster before she could speak. "Let's do it. Milan, you take Ciel-san inside to find Zero. The rest of us will stay out here to buy you time."

"B…but!" Ciel protested. She didn't want any more of her friends to die. They were Reploids, but they were still sentient and were alive.

"Twenty of us have died on the way here," Geai, a female Reploid, replied in a determined voice. "We can't let their sacrifice go to waste. You should go! We'll take care of them until you can wake Zero up. Once he wakes up, he should be able to help us break out."

Ciel wasn't too sure about that, but she was abruptly pushed to the side.

"Enough talk. Stay back, Ciel," Milan said as he fired his buster, effectively ending discussion.

Boom! Wham!

The doors blew apart and fell to the ground after several shots from the soldiers' busters.

"Let's hurry," Ciel urged as she ran forward with newfound resolve.

If her friends were going to lay down their lives, then she had to try her best as well. She wasn't going to idle around and squander the time they were buying for her.

"Huh?" Ciel gasped as they walked in. The entire room was covered in strange runes and symbols that were glowing with an eerie blue light. "What is this place? I've never seen such characters before! This place looks hundreds of years old!"

"Look!" Milan pointed a large statue in the middle. The statue appeared to be a nine-eyed humanoid figure that was sitting in a meditative position. Ciel hadn't noticed it because she had been too engrossed with the glowing characters around the room. "There's a person sitting at the very bottom of the statue!"

The said person was clothed in red, black, and orange and was also sitting in a meditative position.

"This must be…Zero…" Ciel said in awe. Even she could feel the power emanating from the person in front of her. The energy field was obscuring her vision and she couldn't see the figure too well, but circumstantial evidence supported that this was Zero. The reports written during the Elf Wars described Zero having red and black armor.

"We found him at last!" Milan said with a sigh of relief. "Let's wake him up." Milan walked forward and was repelled by a strange energy field. "Waaahh!"

"It's protected," Passy analyzed as she spun around the figure, "with a power greater than what a buster can destroy," she added when Milan raised his buster.

"What should we do?" Milan asked worriedly. "We don't have much time. Our friends won't be able to hold on much longer."

Milan's words proved to be prophetic.

"AHHH!"

Ciel and Milan swerved around quickly and looked back towards the entrance. The sight of dozens of Pantheons chilled their hearts. The Resistance soldiers had fallen quickly and the Pantheons were now marching in.

"We're cornered!" Ciel cried.

"Ciel! Watch out!" Milan cried as he pushed Ciel to the side. "Arrghh!"

"Milan!" Ciel screamed as several energy bullets tore Milan's body apart. "Milan! No!"

"Ciel…" Passy said.

Ciel didn't replied and fell down on her knees in grief. It was a small stroke of luck that Milan had pushed her behind Zero and the energy field protecting him because the energy field was repelling all the energy bullets fired in her direction. But Ciel didn't even have the presence of mind to know what was going on. One of her closest friends in the Resistance had just died.

"Ciel!" Passy urgently slammed into Ciel's head.

"Huh?" Ciel looked up, tears still streaming down her face.

"You should use my power to open up the energy field and revive Zero!"

"What? Passy…if I do that, you'll be…"

"You have no choice! Look!" Ciel stood up and looked back. The Pantheons apparently realized that ranged attacks weren't going to work and started marching warily towards her. "Don't worry about me," Passy urged. "Remember, everyone is waiting for your safe return!"

"…okay," Ciel said after a quick moment of thought. It was horrible of her to accept yet another sacrifice from her friend and she was shamed to admit that the sudden fear that gripped her heart at seeing the sea of blue coming towards her play a role in her decision. "Thank you."

"No. I should thank you, Ciel," Passy replied with a smile. "Don't feel guilty, Ciel." Passy gave her a knowing smile. "I know you too well, Ciel. I do this of my own accord. Live and continue to fight for peace. Farewell, friend."

"Passy!" Ciel cried as the Cyber-elf charged into the energy field.

Boom!

The blast of energy that resulted knocked her and the Pantheons in the room down. Instantly, the glowing runes stopped glowing and the lights in the room came on.

She opened her eyes to see a blood-red cloak with black flames on the bottom. Her eyes roamed up. Blond hair. Red armor.

"Zero…has been resurrected," Ciel concluded. "Zero," she pleaded, "help me. Please."

"Zero?" The figure in front of her replied as he slowly turned around. "I'm not this Zero you're looking for."

Ciel gasped when she saw that the person was human. Normally, it was incredibly difficult for people to tell the difference between an unarmored Reploid and a human being. Technology had come a long way in making Reploids look and sound as human as possible. Reploids had red electrolytic fluids and body chips much in the same way humans had blood and organs. Civilian Reploids even had synthetic skin that even imitated human skin to such a degree that almost no one could tell the difference. But Ciel was the foremost expert on Reploids of the era. She knew when she was looking at a Reploid and when she was looking at a human.

In fact, it was just a boy barely a year or two older than she was.

"You're…you're…" she stammered.

"Later," the boy's eyes narrowed as he saw the Pantheons and their busters. "I don't know what's going on, but I get the feeling that someone I once knew would roll around in his grave if I didn't help a damsel in distress."

"But, you're only human!" she argued. "These are combat—"

Her protest died when she saw the boy make strange hand movements and then summon a violent windstorm out of nowhere. "Fuuton: Reppuu (Wind Release: Gale)!"

"Im…impossible…" she breathed out in disbelief as winds raged around the room.

Within a few seconds, every single Pantheon in the room had been shredded to pieces. But Ciel was so shocked that a human somehow displayed such fantastical powers she didn't even react.

The boy grabbed her hand. "Come on! We have to break our way out of here!"

"Uh…yes!"

They ran out the double doors. To Ciel's continued amazement, the boy punched, kicked, and even occasionally slammed some sort of energy ball called Rasengan at any Reploid that got in their way. He somehow did this while deflecting any energy bullet that would stray her way.

"Eww, disgusting…what are those things?" the boy pointed at a bunch of spider-like Reploids that were jumping out of a nest-like object.

Ciel involuntarily grabbed Naruto's hand tighter. She was a Reploid scientist and had seen all sorts of Reploids, but she was also a young girl and did not like spiders. A lifetime of training did not completely remove the evolutionary programming for humans to hate such creatures.

She responded as professionally as possible, however, instead of screaming and running away like her instincts kept telling her to. Fortunately, the boy's calming presence helped to mitigate those instincts. "Those Reploids are Hoppiders. They create Kumouteru, those nest-like structures, to replicate inside and build up their power. Don't bother attacking the Kumouteru; those are almost completely impervious to physical damage."

The boy turned around and grinned. "Well, can they repel fire?"

"Fire?" Ciel repeated. "You can't possibly mean…"

But he did.

"Katon: Hiendan (Scarlet Fireball)!"

After about thirty more minutes of intermittent fighting and running, they finally reached where an entrance should have been based on the digital map that Ciel had created before entering the laboratory. "What?" Ciel walked up to the newly created concrete wall. "It's a dead end! The Neo Arcadian soldiers must have walled it off to prevent us from escaping." She looked back at the blond boy. "What should we do?"

The boy didn't answer her question because the ground beneath her crumbled. "Watch out!"

"Ahh!" Ciel screamed as she fell. Ciel closed her eyes, but felt the boy catch her in his arms.

When she opened her eyes, they were sliding down the side of the hole. "I can attached myself onto walls," he answered her unasked question. He frowned as they continued sliding down the very deep hole. "Clearly, I must have been asleep for a very long time if such things surprise you."

"If you don't mind me asking…who are you?" Ciel asked as she grabbed onto him tighter. She wasn't entirely sure about the boy's ability to attach onto walls, but it was much better than falling at rapid speeds towards a hard ground. "I had been under the impression that a powerful warrior named Zero was trapped in this underground laboratory."

"My name is Naruto," the boy replied before furrowing his brow. "I can't remember my family name though. A lot of my memories are incredibly fuzzy. But I do know that I was sealed away as a compromise between five large nations."

"Sealed? A human can be sealed?"

"Yes, through fuinjutsu." Ciel didn't know what that was so Naruto's answer didn't exactly clarify anything. She hypothesized that it was some sort of ability akin to those he had shown already. "I was considered too powerful for any single nation to keep, you see," the boy smiled sadly, "and for the sake of peace, I had to be sealed away and be removed from the world altogether."

"That's…that's horrible…"

The boy chuckled. "There are far worse things than being exiled and being forced to wake up many years after your time…um…what is your name, miss?"

"Ciel," she supplied, realizing that she hadn't introduced herself.

"Ciel," Naruto slowly repeated, as if tasting the name in his mouth. "Well, I have plenty of questions to ask, but it'll have to wait. It looks like we're at the bottom."

Naruto took a small hop off the side of the wall and landed on the ground before setting Ciel on her feet.

"Thank you," Ciel said as she smoothed out her pink skirt. "Based on what I see here, this place is an old laboratory. We may be able to find a Trans Server, which we can use to go back to the Resistance Base."

"I'm not sure if I understood much of that, but there seems to be a passage way over there." Naruto pointed to a hole in the wall to their right. "Let's go."

After about ten minutes of running, they reached a dead end.

"How nice," Ciel said in an uncharacteristically sarcastic voice. She was sad, tired, irritated, and confused from everything that had happened in the last few hours and lost a bit of control. "This passageway is collapsed in. Shall we go back and look for another way?"

"Wait!" Ciel jumped at the sudden warning. "Get back!"

She made to move towards Naruto, but a large mechanical hand burst through the rubble and grabbed her.

"Naruto-san, run!" Ciel cried. "We must have triggered the security system of the ancient laboratory earlier when the floor collapsed earlier! Even though it's an outdated version, it's still a Golem. Its combat prowess is far superior to the Reploids you've already beaten!"

Naruto gave her a look of incredulity. "Weren't you listening at all? I was sealed away because I was too powerful. I'll save you. I promise."

He had promised to save Ciel, but he wasn't entirely sure how he would go about doing it.

To be sure, Naruto could take down the Golem with ease, but it would be something else altogether to try and beat the Golem without hurting Ciel. Unfortunately, most of his jutsu, at least the ones he recalled, were tremendously powerful area of effect attacks. Naruto didn't have a single weapon on him and because of the Golem's thick armor, normal taijutsu would be next to useless.

Rasengan was his best bet. It didn't cause particularly surgically precise damage that the Chidori could, but the damage was still limited to a relatively small area.

Naruto's eyes widened when the Golem shot out some sort of green energy beam.

"Oh crap!" Naruto dodged to the side, but felt the laser burn through part of his cloak. "Damn, that thing itself is slow, but its attacks are incredibly fast." Naruto almost face-palmed when he saw the Golem slam itself on the wall. "It doesn't seem to be particularly smart though," he muttered to himself.

That would work in his favor. It most likely wouldn't use Ciel to force Naruto to surrender.

Naruto dodged the falling rubble that had been dislodged by the Golem slamming itself on the wall. Naruto looked back at the Golem. Maybe the Reploid wasn't so dumb after all; the body slamming must have been a way to dislodge the stones from the ceiling.

"Naruto-san! Its weak point is its head!" Ciel shouted out. "Aim for the top of its head."

Naruto whistled. The girl had managed to analyze her enemy while being under a stressful situation. Ciel was physically fragile, but her mind was sharp. Naruto had no doubt that she had seen her fair share of battle.

"Tajuu Kage Bushin no Jutsu (Mass Shadow Clone Jutsu)!"

Naruto smirked as several dozen clones popped up into existence and set his plan into motion.

"I'm not sure if I'm ever going to stop getting impressed," Ciel whispered to herself in amazement. "I've heard that Hidden Phantom could create illusory clones but…these are solid clones!"

It wasn't just the older boy's abilities that baffled her though. There was an unusual aura of security and confidence around the boy that drew her to him. With just few words, he had managed to bring hope back into her heart again. Hope that she had thrown away when she had fallen and again when she had been caught by the Golem.

Ciel watched was the solid clones charged towards the Golem and threw themselves forward. The Golem, though not recognizing that they were clones, destroyed them nonetheless. For the Golem, any moving object was immediately labeled as a hostile.

Ciel coughed as all the clones were dispelled into smoke. So that's what he was going for. Ciel realized. He created a smokescreen to blind the Golem so he could get close without being detected.

When the smoke cleared, there was no one in sight.

The Golem swerved its head around from side to side looking for any potential threats. After a few seconds, satisfied that it had gotten rid of Naruto, it began to squeeze and crush Ciel.

She struggled to breathe and shifted her body around. She needed to hold on until Naruto could destroy the Golem.

"Rasengan (Spiraling Sphere)!"

Naruto and a clone fell from the ceiling and each slammed an energy ball into the Golem: one into its head and the other into its arm.

Ciel immediately felt the Golem's grip relax and fell into Naruto's arms. "Hurry," she gasped out. "When powerful Reploids die, they release a huge burst of energy."

"You mean it's going to—"

BOOM!

The explosion instantly blinded them both. When her vision came back, she found herself still in Naruto's arms but now inside a strange barrier.

"Suiton: Suirou (Water Release: Water Tower)!" Naruto muttered quietly before glaring at her. "It took quite a bit of chakra trying to activate it without any seals in an area with no water. You could have told me that it was going to explode before I destroyed it."

Ciel wilted in his arms under his harsh glare. "Ah…sorry, Naruto-san. It slipped my mind."

Naruto blinked at her for a few seconds, almost as if he was confused that she wasn't protesting and arguing back. He started laughing. "Haha. Relax! I was just joking. I don't blame you." Ciel felt a bit put out when he took that moment to set her down. She knew it was irrational of her, but she had felt secure and safe in his arms. "It's understandable that you forgot. You were a hostage, after all. All things considered, you were amazing, considering that you were able to figure out where the weak point on that bucket of bolts was. I wouldn't have been able to beat that thing so easily otherwise."

Ciel felt her face go hot. Gratitude? Pride? No. It was neither of those. Whatever she was feeling was something new altogether.

"Eep!" she managed out before covered her mouth in embarrassment. Confidence wasn't ever really her strongest trait, unless she was talking about an academic topic, but she never fell apart like this.

"Eh?" Naruto asked before smiling again. "Well, Ciel, and I hope you don't mind if I keep things informal," he added and Ciel shook her head, "you haven't really finished telling me about yourself."

She paused to figure out where to begin. "Well…I already told you my name. My name is Ciel. I am a scientist, more specifically a scientist in Reploid technology."

Naruto whistled in appreciation. "A scientist at that age? You must be what…fourteen? Fifteen?"

"I will be fifteen in two weeks."

Ciel wondered why she supplied that information to a near stranger even if he had saved her life. Moreover, she was confused why he had asked. It wasn't like her birthday was particularly meaningful anyway. In this world, the only thing that mattered was survival.

This boy, however, seemed to think otherwise. He was full of life and his energy and excitement began to bring out an unfamiliar feeling from within her.

"Wow, see! That's young! I thought scientists were supposed to be really old! Don't you normally have to study for decades to become a scientist?" Naruto smiled. "You must be incredibly smart!"

"Ah…well, it…it would be more accurate to say that I was designed to have high intellect." Ciel was pleasantly surprised by the compliment but was humble enough to brush away the compliment.

Naruto suddenly became serious. "Designed? What do you mean designed? Like test-tube babies created in experiments?"

"Yes," she answered. "I am a part of a group of humans called the Enlightened Ones. Before we were born, our genes were optimized so that we would function more efficiently than normal human beings."

For a second, Ciel thought that she had angered Naruto because the air around them grew thick for a split second. She even took a faltering step back. But before she knew it, the ominous aura was gone. "Hm...so you were created? Are people being created even now?"

She shook her head. "No. As you can imagine, there were ethical issues with designing and creating humans. Furthermore, many people were unhappy that some humans were blessed with higher intellect and physical capabilities at birth. Humans were fine with Reploids being smarter, stronger, and longer-lived because Reploids were and are subordinate to humans. But creating an elite group of humans proved to be incredibly unpopular with the public. The practice of creating the Enlightened Ones stopped after one generation of ten children. I happened to be one of those children."

"I see," Naruto said with an unreadable expression. "Well, I think that's enough for now, Ciel. You mentioned something about a Trans Service earlier?"

"A Trans Server," she corrected. She walked over to a nearby computer. "I recognize the model of these computers. They were made in the last hundred years so there should be a Trans Server nearby. Trans Servers have been in use for two hundred years now." She led him to a nearby door and walked into the room. "See? We're in luck. There's a Trans Server here."

Naruto walked over and touched the apparatus. "So how do we use this thing?"

Ciel frowned. "Well, we'll have to reactivate the Trans Server somehow. Clearly, judging from the fact that some of the lights are on, there is still electricity running through the place. We could redirect the energy to the Trans Server. But it might take some time. We'll have to hope that enemies don't find us down here."

"Electricity?" Naruto asked as he held up a glowing hand charged with electrical energy. "What if I could provide the electricity?"

Ciel almost gaped at him before shaking her head. "I did promise myself that I wouldn't be surprised by anything you did anymore. You seem to be able to do just about anything, Naruto-san."

"Naruto," the boy insisted as he directed the energy in his hand to the power source of the Trans Server. "Call me Naruto. I know I'm older than you and you seem to be a proper girl, but I hate formalities."

"Very well, then…Naruto," Ciel replied with a small smile. "And once again, thank you for saving me."

Naruto's Jutsu List

Technique: Fuuton: Reppuu (Wind Release: Gale)
Rank: B-rank
Class: Offensive
Range: Mid to Long Range
Description: The user swipes their hand in front of them causing a massive burst of pressurized air to come forth. The wind may be either blunt or sharp depending on what the user intends.

Technique: Katon: Hiendan (Scarlet Fireball)
Rank: B-rank
Class: Offensive
Range: Mid-Range
Description: As with most fire techniques, the user takes in a deep breath and blows out a ball of fire. Unlike standard techniques, the fireball is a condensed ball of white fire in the middle with brilliant red flames, serving to limit the heating radiating from the fireball.

Technique: Tajuu Kage Bunshin no Jutsu (Shadow Clone Jutsu)
Rank: B-rank
Class: Supportive
Range: N/A
Description: The user creates a clone construct using chakra. The user's chakra pool is evenly and continuously divided into all active clones. Dispelling clones returns unused chakra within the clones and immediately ends the splitting effect on the user's chakra pool.

Technique: Rasengan (Spiraling Sphere)
Rank: A-rank
Class: Offensive
Range: Short Range
Description: A powerful attack created without the use of hand seals. Rasengan is created through the accumulation, amplification, and containment of multiple sets of rotating chakra in the user's hand. Rasengan doesn't have much piercing power, but may cause massive internal trauma through the transmission of its rotational force into the victim's body.

Technique: Suiton: Suirou (Water Release: Water Tower)
Rank: B-rank
Class: Defensive
Range: Close Range
Description: The user may use a nearby water source or create the water using a significant amount of chakra to form a water bubble around them to be used as a barrier or around a specific target to be used as a prison. Unlike the Water Prison Technique, however, the inside of this technique is not filled with water. The chakra that runs through the water makes it impenetrable to most physical and chakra-based attacks.