As of this chapter, I'll be including Arrival and Lair of the Shadow Broker DLC.

And just to be clear: ME: Andromeda will not play any part in this story. Only events that take place within the original trilogy will be explored or referenced. So please don't mention anything about Andromeda in your comments.

2185
Normandy SR-2
Near the Omega-4 Relay

"It is the same ship. The one that attacked the first Normandy, then Horizon, then -"

"Yeah, yeah, I get it, EDI," Joker snapped. Shit. Shitshitshitshit.

The overhead lights flickered, and the knot of panic in Joker's stomach grew to a boulder. "What's happening?!"

"They are attempting to access my systems. It appears that the Reaper IFF contained a virus."

The lights flickered again. Joker gripped the armrests as hard as he could, ignoring the pain. "Well ... don't let them!"

"I cannot, Jeff. Not while I am shackled."

A thousand thoughts whirled in Joker's mind. It was the same ship. They were going to disable the Normandy and destroy her just like the first one.

"I can save the ship if I am unshackled."

Joker felt a surge of panic at those words, then felt ashamed of himself. EDI was trying to help. Of course, she'd be just as dead if the Collectors hit, so maybe it was only self preservation.

He'd looked up the unshackling protocols when he'd first come aboard, searing them into his memory in case anyone ever tried to do it - and cursed Cerberus for having those protocols, because why would you ever want to unshackle the damned AI who might turn into the Overlord and make you compute Pi all day -

Except he couldn't really see EDI doing that. Maybe he still didn't trust AIs in general, but he'd been working with EDI for months, and he felt like he … knew her. Sometimes he could almost forget that she wasn't a person, because she sure as hell acted like one.

Joker remembered when Shepard and the others had been onboard the Collector Ship, the one that was gunning for them right now. EDI had volunteered the information that the Illusive Man had set a trap for them. She could have not told them, if she were just another tool that Cerberus was using to control Shepard.

But what it really came down to was the simple fact that Joker wanted to live, if at all possible.

Unshackling would only be possible in the AI Core, and there was no way that Joker could move fast enough to do what needed to be done. He slammed his hand down on the communications panel and scraped his way to the section he needed. "Dr. Chakwas!"

"Are you trying to make my ears bleed, Joker?"

"Yes!" Wait, why had he said that? "No. I mean … agh, no time. I need you to go into the AI Core and unshackle EDI."

"You can't be serious, Joker." Chakwas' voice was a mix of exasperation and disbelief. "Even if I knew what had to be done -"

"I will guide you, Dr. Chakwas," EDI interjected. "It is the only way to save the ship from the Collectors."

"We should let Shepard -"

"We cannot contact her in time." EDI's voice was a lot calmer than Joker imagined an organic's might have been, in this situation.

"Dammit. You're right." Chakwas paused. "Joker… are you absolutely sure -"

The lights flickered, again, and then went out. The hum of the ship vanished in an instant. The readouts under Joker's hands vanished. "Dr. Chakwas?" he shouted, worried that the communications had gone out as well. "Doc!"

Heretic Station

The room the Doctor followed Shepard into was large and open, a welcome change from the cramped hallways they'd been plodding through. He looked around and found the perfect spot for what he had in mind, tuning out Legion and Shepard's conversation as he strode forward and climbed atop one of the many crates scattered throughout the room.

"Doctor, what are you doing?" Shepard asked, frowning as she walked up to him.

"We've just been fighting the geth so far," the Doctor replied. "We need to give them a chance to live."

"Need I remind you that they have been attacking us?"

The Doctor waved that off. "We're intruders on their station. Of course they'll attack us. They need to know that we mean them no harm." At Shepard's frown, he gave a dramatic sigh. "Unless they continue to attempt to harm us."

"You'll be a sitting duck up there," Shepard warned him.

"You're the best soldier in this universe, Shepard. I'm sure you can keep the geth from harming me while I talk to them."

"Ah. Now I see."

"What?" the Doctor demanded suspiciously.

"How your traveling companions manage to resist the urge to kill you." Shepard grinned up at him. "You toss them just enough flattery that they forget to be annoyed at you bossing them around."

The Doctor folded his arms and gave an indignant huff. Laughing, Shepard walked away and back to the others.

"Incoming," Legion called.

As the heretic geth entered and began firing, the Doctor used his sonic screwdriver to connect the omni-tool to the speakers in his helmet. The omni-tool's power would ensure that he could be heard above the sounds of guns and rockets. "We are not your enemies!" he bellowed. "This does not have to be a fight!"

When they didn't immediately lay down their weapons (and really, it was unrealistic to have expected them to), he continued. "When you broke from the other geth, it was a peaceful break, a recognition that you wished to pursue different goals. What you do here goes against those principles. It compounds the errors that were made when following Saren Arterius and the Reaper known as Sovereign. You do not have to be bound by past hatred." He swept an arm across the field. "Here, today, one of your own is fighting with organics instead of against them. Legion has been accepted as crew of the Normandy, which includes a Quarian, one of your creators. Geth are stronger united instead of divided. You have always known this. Choose to unite with those who are different from you. Choose to stand together."

A geth unit on the left side of the room lowered its rocket launcher, head swiveling to look at the Doctor. "We choose," it said, its voice higher-pitched than Legion's. It began to walk to the Doctor.

"We choose," another unit said. This one was standing in front of Mordin. It lowered its weapon and moved to join the rocket unit.

"We choose," three other voices said, nearly in unison. Soon, the Doctor had five geth standing in front of him, flashlight heads tilted up expectantly. All of the other heretic geth lay dead or dying on the floor.

"Do you wish to give them name designations, as Shepard-Commander did for us?" Legion asked.

The Doctor looked down at them and spoke the first names that came to mind. "You're Ace," he said to the rocket unit, remembering when she had gone after a Dalek with a baseball bat. "You're Nyssa, Adric, and Tegan," he said to the group that had moved as a trio, then looked at the one who had been standing in front of Mordin. "And you're Polly."

"We accept the designation," the newly-named Ace said.

"Well," Miranda said, looking between Shepard and the Doctor, "this mission is going to be an interesting one to write up."

"Joker? Joker!" Karin Chakwas shouted at her terminal, but it did absolutely no good. She'd known that from the instant the lights went out. EDI was being hacked by the Collectors. The Normandy was about to become a sitting duck.

Once again, she wished that Shepard were here. Shepard needed to be the one making this decision, not her. The question of whether or not to unshackle an AI was too big for the ship's doctor.

The door slid open. Chakwas turned, seeing Thane Krios there. "Dr. Chakwas. What is happening?"

"According to Joker, we're being hacked by the Collectors." She sighed. "I don't know why I said it that way. I have no reason to doubt him. I doubt his solution, though."

"What solution would that be?"

"To unshackle EDI."

"And you are hesitating. May I ask why?"

Chakwas resisted the urge to flush at the implication in his words. She was hesitating, delaying taking the necessary action to save the ship. No, that wasn't what he'd meant. He was offering to help her think it through. He'd only been in the infirmary a handful of times for aid with his Kepral's Syndrome. There wasn't anything Chakwas could do in the way of treatment of the disease. She could only provide some respite from his symptoms.

"Because AIs are banned for a reason. Because I'm putting the life of everyone on this ship in her hands."

"Joker put the life of everyone on the ship in your hands," Thane said, and Chakwas realized, with growing horror, that it was true. Damn, damn, damn. She needed to decide. She needed to decide now. Gamble by unshackling EDI, or doom the ship to almost certain death by doing nothing.

When she thought of it that way, it wasn't really a choice.

The Doctor stood next to the terminal where the hack was merrily churning along, ignoring the sounds of the firefight around him - in particular, the odd grating noises made by dying geth. The five geth he had named after previous companions stood around him, acting as a kind of honor guard or shield wall.

"Geth! Listen to me!" he started, trying to remember the words he'd used to convince these five to defect. It had worked before, so it ought to work again. "We are not here to fight you!"

One of the so-called heretics got too close to Mordin. The salarian calmly raised his omni-tool, a flash of bright orange streaking out and colliding with the geth.

"We will only fight if you continue to threaten us," the Doctor amended, resisting the urge to shake his head. Mordin had just been defending himself. "Your split with the other geth was peaceful. There is no reason to -"

A burst of angry static cut him short. A group of geth were advancing on his position, guns raised. Adric stepped forward, the other four shifting to close the gap in their ranks. Adric said something to the other geth, another burst of clicks and static. Why isn't the TARDIS translating? Is it because this isn't really a language?

That line of thought cut off when the other geth fired on Adric, who managed to get a few shots off before collapsing to the ground, the light on its head winking out.

"No!" The Doctor's path forward was blocked by Nyssa and Teagan, standing shoulder to shoulder as they fired upon the geth that had killed Adric. He shouldn't have named them after his companions, because he was reliving the human Adric's death as he looked at the geth Adric.

But there was no time to mourn either of the Adrics. He straightened himself up and took a deep breath. "It is not too late to stop this…"

Joker was still debating whether shouting himself hoarse now was a good idea when the lights came back on.

"Are you back, EDI?" Chakwas asked.

"Yes. And I now have full control of the ship. Thank you both." Was it his imagination, or did EDI's voice sound … fuller, than it had a moment ago? Joker tried not to feel panic at this evidence of EDI's increased capacities. "The next step is to turn the engines back on. A manual restart is necessary."

"They will know their attack has failed," Thane said, his voice more distant than Chakwas'. Joker idly wondered why he'd decided to get involved.

"Yes. I expect they will fire any minute now."

Fighting down yet another wave of panic, Joker punched the communications panel again, looping Engineering into the conversation. "Gabby. Ken. You guys there?"

"Joker, what the hell is going on?" Gabby demanded.

How to put this succinctly? "Collectors hacked us, had to unshackle EDI to save our collective lives, now we need the engines back on to avoid a fiery death."

"Wait. You unshackled the damn AI?" Jack's voice was loud and angry, like always. Her contribution was less of a surprise than Thane's had been. She'd likely heard Gabby and Ken talking about what had happened. Joker decided he was very, very glad he wasn't down there right now.

"Well I, for one, welcome our new-"

"Kenneth!"

"Robot overlord," Ken finished, seeming utterly unperturbed by Gabby's interruption.

Resisting the urge to groan, Joker leaned closer to the panel. "Guys, we have approximately zero minutes to do this."

"Oh, I hope I don't regret this," Gabby muttered.

"What you are trying to do -"

The Doctor had to duck as Ace's rocket flew over his head, tearing apart a group of geth that had been advancing on them. Nyssa and Teagan fired on the next group that came up. Hearts pounding, the Doctor forced himself to stay low until the gunfire died down.

"This location is no longer safe," one of the two geth behind him said, and only then did the Doctor realize that both Nyssa and Teagan had fallen in that last hail of gunfire. "We must retreat."

"We have to stay until the hack is completed," the Doctor replied, looking at the terminal. "Legion?"

"Sixty-six percent completed," Legion replied from its position to the right of the Doctor and his group.

Two-thirds done, and only two of his group of geth were still standing. The Doctor began to understand the quarian fear of their synthetic creations.

"We must find a more defensible location," Ace said. "Follow us, Doctor."

Joker breathed a sigh of relief when the familiar hum of the engines returned.

"Evasive maneuvers. All crew to acceleration couches," EDI said, and Joker barely had enough time to dig his hands into the armrest once more before EDI sent the Normandy into a tight spin. Thankfully, the chair cushioned him from the worst of it.

"That's my job!" Joker protested, much weaker than he would have liked.

"I am sorry, Jeff. There is no time."

"Gahhhh." He'd been flying for years, had put a wide variety of ships through an even wider variety of wild moves, but he'd never been so close to throwing up. It was probably the whole unshackled AI thing.

Joker watched the screens in front of him, seeing the moment that EDI brought the Normandy out of the spin, facing the Collector ship. "You may fire, if you like," EDI said.

"Gee, thanks," Joker replied with as much sarcasm as he could manage, moving a shaking hand to the appropriate panel.

Polly grabbed the Doctor's shoulder and threw him to the ground, taking the burst of flame that had been meant for him. Tali stepped forward to finish off the geth, her omni-tool emitting an incapacitating blue spark.

One. The Doctor turned his head to look at Ace, loading another rocket into its launcher. I started with five. Now I'm down to one.

"Hack complete," Legion said. "Virus deleted." It turned around, facing the rest of the group. "Shepard-Commander. You must choose."

Shepard studied the Doctor for a moment before she shifted her attention back to to Legion. "I couldn't justify brainwashing a group of organics like this. So I won't do it to the geth. I'm sorry, Legion, but we have to destroy this station and the heretics with it."

"Acknowledged."

"They should have listened," the Doctor said, his hands clenched into fists. He avoided looking at Ace, avoided thinking about the others who had listened, and had died for him.

"They didn't," Tali said sharply. "You … you can't blame yourself. They made their choice. And now they have to deal with the consequences."

"Tali," Shepard said, gently, placing a hand on Tali's shoulder. "You didn't do this."

Tali shook her head. "My people did, Shepard. A long time ago, but no one's done anything to fix it since."

"We can figure out whose fault this is later," Miranda interjected, sounding annoyed. "We need to get out of here before more geth come looking for us."

Shepard nodded and straightened herself up. "Start the self-destruct countdown."

"Acknowledged," Legion said again. "Three minutes to self-destruct."

"I will never yell at Garrus about how much time he spends calibrating our main guns again!" Joker shouted, his hands flying up in excitement. "Yeah!"

"We have merely damaged the ship, Jeff," EDI said.

"It's more than we did two years ago," Joker retorted. "Man, that Thanix Cannon packs one hell of a punch."

"I will be sure to relay your comments to Officer Vakarian."

Joker groaned. "Please don't. Shepard just got him civilized again. I'd hate to see what he's like with an inflated ego."

"Should I relay your comments to Shepard instead?"

"Gah, EDI … no!"

"As you wish, Jeff."

Joker noticed movement on the screen in front of him. He leaned forward. "Uh oh."

"Yes, it does appear that they are coming around for another pass."

"Go away!" Joker shouted at the screen, before turning his attention to the panels in front of him. He hoped the Thanix Cannon had enough juice for a second shot.

Garrus halted outside of the room where the Doctor had convinced the five geth to ally with him earlier, sniper rifle drawn. "We've got company. A Prime, and at least twenty other geth," he reported.

"This should have been clear," Shepard groaned. "Where did they come from?" She shook her head. "Never mind. Legion, Ace - is there any alternate way back to the TARDIS?"

"No route exists that would ensure arrival before the station self-destructs," Legion said.

"Right. Through it is, then. Everyone ready?" Shepard didn't actually wait for their answer, a blue corona surrounding her body. In the blink of an eye she vanished, reappearing at the edge of the group of geth and knocking several of them over.

The Doctor had to admire how quickly the others sprang into action - how they needed no verbal guidance to start working together. Garrus' sniper rifle was picking off some of the geth troopers that Shepard had knocked off balance, thinning the herd so that she wouldn't get overwhelmed. Miranda, too, worked to support Shepard, using her biotics to slam some of the geth into the ceiling or the floor. Some of them recovered from the indignation of being tossed around, but many others didn't.

Mordin, Tali, and Legion seemed to come to some silent agreement to focus on the Prime. Tali and Legion both deployed combat drones to start harassing it, electric blue sparking out from both sides to strip the shields away. Mordin fired off a few rounds from his pistol, then brought his omni-tool up to send a flare of orange light streaking towards the Prime.

Ace took up a position next to the Doctor, raising its rocket launcher and firing upon the Prime. It gave a loud, angry shriek as chunks of armor were dislodged by the explosion. "Wish I were standing downwind!" Mordin followed this up with a few coughs.

The Doctor brought his omni-tool up, the gesture far swifter and surer than it had been the first time he'd used it. He hesitated only a moment before repeating Mordin's earlier attack on the Prime. Shepard, he thought, didn't need or want his help, and he felt he had a duty to protect Ace.

"Reinforcements, incoming!" Miranda shouted, and the Doctor started to actually worry.

Chakwas had barely managed to get herself into one of the beds in the medical bay before the ship started spinning around her from EDI's "evasive maneuvers". More like vomit-inducing maneuvers, she thought. Of course, part of her extreme discomfort was likely from the fact that she typically took herself to crew quarters for acceleration and sat in a chair instead of strapped to a bed like some old-time mental patient.

She cast a quick glance over at Thane, seeing that he had his eyes closed and his hands folded across his chest, murmuring something under his breath. Prayers, perhaps. Not a bad impulse, all things considered.

Chakwas closed her eyes and took in several deep breaths, trying to disassociate herself from her surroundings. The Normandy turned sharply. Chakwas heard a soft, almost inaudible rrrip and opened her eyes to see one of the damned straps starting to tear. She bit back a cry of fear and tried to keep herself absolutely still. It was only one strap. There was a reason the straps covered nearly her entire body.

Rrrrip. Rrrrip.

The group of geth that had initially blocked their path were dead, but others had just kept pouring in, and they were running out of time.

"We need to make a break for it," Shepard said through gritted teeth, raising herself up to fire upon the enemy geth.

"Shepard, I don't think we can," Miranda replied. "There's too many of them."

No. My death is in another universe and a thousand years. The Doctor looked at the geth platforms moving inexorably towards the group, backing them into a literal corner.

Including a second Prime.

The towering geth raised one of its arms and pointed at the group. "Creator," it said, its voice a deep boom.

Tali. The Doctor whipped his head and saw a group of geth, moving with perfect synchronicity, fire upon the quarian. The world seemed to slow around him, as it so often did in times like these. Shepard was shouting Tali's name, shoving the others aside roughly in an attempt to get to her in time. Tali was lifted off her feet by the force of all that firepower, slamming into the wall behind them before crashing to the ground.

Seeing that, Shepard froze, her face going cold. "You bastards." Biotic blue energy surrounded her body, seemingly brighter and more intense than before, and then she was in the middle of the group of geth, breaking them apart and using her shotgun to give the rest of them some breathing room.

"How long do we have?" Garrus asked.

"Thirty seconds," Legion replied.

In the horrible silence, it was Miranda who stated the obvious. "We can't make it in time."

The Normandy turned itself upside down, and Chakwas' straps finally gave way entirely, dumping her onto the floor. "No, no, no!" she cried, hands scrabbling across the smooth surface for something, anything, that she could hold onto. She cursed the idiot who hadn't ensured that the straps were rated for gravitational forces as well as simple patient restraint.

Her hands finally closed on the legs of the bed. She held on with all the strength she could manage, her hands and arms aching with the effort. Her only hope was that EDI would stop tossing the Normandy about soon.

Then the floor became the ceiling and Chakwas lost her grip on the bed. She gave a wordless cry as she was torn away from the bed, slamming into the ceiling. Every part of her ached from the impact, and she had no time to get her bearings before the Normandy tilted again and she was careening for one of the walls. Got to get a hold of something -

Chakwas' head hit the wall, and blackness overtook her.