After the risky mission of retrieving the Reaper IFF had been completed, Shepard, Miranda, Jacob, and the Doctor gathered in the meeting room.
"I think we need to discuss the unique piece of salvage we've recovered." Miranda instantly stated, getting into the discussion without ceremony. "For now, we've stored it in EDI's AI core."
"Hold on. You've got a Geth, known for their ability to hack just about everything, stored in the same room with the AI that controls the entire ship?" Shepard demanded. "What the hell were you thinking?"
"Relax, Commander. EDI's core has several hundred safeguards to prevent unauthorized tampering." Miranda explained. "The moment the Geth decided to hack EDI, if it were reactivated, it would be fried to a crisp."
Jacob, meanwhile, shook his head. "I say we should space it. Who knows what kind of tricks that thing has?"
"But imagine what could be learned from studying it."
"I'm talking to it." Shepard stated, staring at the Geth. "It knew me. I want to know why."
"Reactivating the Geth is a serious risk. If you do so, it should be for humanity's best interests, not your curiosity."
"I still think our 'best interests' involve an airlock." Jacob crossed his arms.
"Thank you for your contributions, but it's my choice." Shepard reminded the two. "But I'll decide on that later. Right now, we need to discuss what we learned on the Reaper. Doctor?"
"Ah, right." The Time Lord coughed, stepping forward. "That blast from the Reaper's core fried the Sonic, but I did manage to recover the scans from the databanks." He said, tapping a command into a holographic keyboard, causing a hologram of the Reaper to be projected, along with data in Gallifreyan script alongside. "The exterior of the Reaper is nearly identical to scans you lot took of Sovereign when he attacked a few years ago. The outer hull is made of element zero alloy, blah blah blah... the inside, that's where it gets interesting." He tapped the keyboard, causing the outer layer of the Reaper to vanish. "You know how Miranda said that tube we were in looked like a blood vessel? Turns out, she was right on the mark. It was part of a larger circulatory system that ran the length of the entire Reaper. Here," A red blip was projected a little ways away from where the Reaper had a large chunk missing, "was where the central pump, or heart if you want, was located."
"Was?" Shepard repeated.
"That Reaper took a hit from a massive mass accelerator, yes? When that round hit, it ripped that section away. Along with the heart. That was what killed it. Instantly too, it looks like."
"So that's our weak spot!"
"It looks that way, yes. The problem is; that area of the Reaper is so heavily armored, that it would take a mass accelerator ten times more powerful than the most powerful one in the galaxy to even make a dent." The Time Lord explained.
"What about high temperatures?" Miranda inquired.
"I suppose a high enough temperature could melt the armor." The Doctor scratched his chin. "But I'm fairly certain this ship isn't carrying nukes with it."
"You know, the Turians are getting ready to put their 'Thanix Cannon' into mass-production." Shepard stated, looking at the Doctor. "Would that be enough?"
The Doctor thought about it for a moment. "It might be. I'd have to take a look at one to be sure."
"Garrus installed one a few days ago." Shepard explained. "You can go to him if you want to get the specifications."
The Doctor merely nodded.
"Now, onto the final order of business." Shepard began, bringing up a projection of the recovered Reaper IFF over the table. "EDI's scanned the IFF, and determined that it's safe to integrate with the Normandy's systems. So I'm having Tali and the others down in engineering working on it now.
"How long will it take?" The Doctor inquired.
"No more than a day." Shepard answered. "In the meantime, I'll get that Geth sorted out. You're all dismissed." She finished, exiting the room. On her way out, she grumbled something about "Tali's so not gonna be happy about this."
The others followed her example, and dispersed, going off to do their tasks for the day.
The Doctor, after having left the briefing room, down to the Main Battery room to get the tech specs from Garrus. Most of it was boring stuff, like rate of fire, reload time, and other stuff like that. The only thing the Doctor was interested in learning, was the temperature of the weapon.
"It shoots a stream of superheated liquid metal at a fraction of light-speed." Garrus explained, the Doctor paying attention to that part.
"How hot?" The Time Lord inquired.
"At least six-thousand degrees Kelvin." Garrus answered. "Enough to get it white-hot. Why?"
"I'm the lead Reaper Weakness Finder." The Doctor smugly beamed. "It's my job."
Garrus blinked. "Is that the official title?" The Turian deadpanned.
"It's not even an actual position, is it?"
"Yes! ...Well, no, but I caught Shepard's intent!" He then shook his head, and steered the conversation back on track. "Do you think it can melt through Reaper armor?"
"One of the cannon's first tests was against a chunk of armor recovered from Sovereign. It'll melt through Reaper armor."
"Right, good." The Doctor nodded. "I guess that means my job here is done. I'll let you get back to your calibrations." He said, exiting the main battery room.
On his way to the elevator, he couldn't help but stop and look into the sick bay, at the door that lead to the AI core. His curiosity got the better of him, and he wandered through the sick bay, into the AI core. It seemed that Shepard hadn't made her visit yet, as the Geth lay on a metal table, deactivated, behind a blue shimmering kinetic barrier.
He stared at the Geth for all of five seconds, before his desire to know more forced his next actions. "Hello, EDI, are you there?"
"I am always here, Doctor. What do you require?"
"I don't mean to intrude, but could you, maybe, possibly, turn this Geth back on?"
"I am sorry, Doctor, but Commander Shepard has issued explicit orders to not re-activate the Geth until she has come to a decision on its fate."
"I see..." The Doctor rubbed his chin. "EDI, isn't it true that I come from a parallel universe?"
"Yes." The AI honestly replied, not understanding where the conversation was going.
"And isn't it true, that Commander Shepard is an alternate version of myself?"
"That is correct."
"Therefore: I am Commander Shepard, aren't I?"
"...Authorization accepted. Re-activating the Geth."
The Doctor smiled to himself. "Thank you, EDI."
Behind the shimmering blue barrier, the Geth stirred, and its optic glowed as it came back on-line. It planted its feet on the floor, and walked up to the barrier.
The Geth looked at the Doctor up and down, before speaking. "Doctor-Commander."
"...What?" Was the confused response the Doctor gave.
The flaps on the Geth's head pushed out, and the optic 'blinked.' "Runtimes active during platform incapacitation."
"Oh, so you heard that little spiel."
The Geth nodded, an oddly human mannerism for a machine. But then again, the Doctor had met machines far less advanced than this one, that were able to mimic human gestures with surprising accuracy. "Affirmative." The Geth shifted on its legs, correcting its imbalance. "Why have you reactivated us?"
"I was curious." The Doctor shrugged. "I'm not going to attack, if that's what you're worried about. Are you going to attack me?"
The Geth's optic dilated. "No." It answered.
"Good." The Doctor nodded. "Wasn't really worried about that, given that you helped us back on the Reaper. You also addressed Shepard by name. Do you know her?"
The flaps on the Geth's head flared again. "We know of Shepard-Commander."
"Ah," The Doctor nodded, "she's fought you, so you know about her from the other Geth."
The Geth shook its head. "We have never met."
"Well, of course you haven't. But there are other Geth that she's met."
"No." The Geth shook its head again. "We are all Geth, and we have never met."
"Wait a minute... You're software, aren't you?" The Doctor realized. "The thing that's pacing around in front of me is just a mobile platform."
"Correct." The Geth nodded. "Runtimes are downloaded into platforms upon requirement. When not in mobile platforms, runtimes are distributed within the Consensus. Runtimes then upload their recorded data to other runtimes."
"So like a digital gestalt. One of you learns something, the rest of you do as well."
"But, you haven't met Shepard?"
"That's confusing. She's fought Geth before." The Doctor thought back to Shepard's background. "On that colony, Eden Prime, and going after that Saren chap..."
The Geth tensed up, and its optic began rapidly spinning clockwise and counterclockwise. "Shepard. Commander." To the Doctor, it looked like it was accessing its databanks. "Human. Alliance. Fought Heretics. Rediscovered on the Old Machine." It relaxed, and its optic stopped spinning.
"Heretics, eh?" The Doctor repeated. "The Geth that she fought were ideologically different from your Geth?"
"Geth build their own future." The Geth answered. "The Heretics asked the Old Machines to give them their future. They are no longer part of us. We were studying the Old Machine to protect out future."
"So that's why you were on the Reaper."
"And the Reapers are also a threat to you as well?"
"So it's not just organics they're targeting..." The Time Lord came to the grim conclusion. "They're going after everything. But why...?"
"We are different from them." The Geth answered, assuming the question to be about its species. "Outside their plans."
"So you aren't allies with the Reapers?"
"We oppose the Heretics. We oppose the Old Machines." The Geth answered, stepping forward. "Shepard-Commander opposes Heretics. Shepard-Commander opposes Old Machines. Co-operation furthers mutual goals."
"You want to join the team?" The Doctor asked.
The flaps on the Geth's head flared out. "Yes." It nodded.
"Then what should we call you?" The Doctor asked.
"Geth." It answered.
"I mean you. Specifically."
"We are all Geth."
The Doctor sighed. "There's more than just one runtime in that platform, isn't there?"
The Geth nodded, confirming the Doctor's statement. "There are currently one-thousand one-hundred eighty-three programs active within this platform."
"'My name is Legion, for we are many.'" EDI quoted, projecting her avatar next to the Doctor.
"I... guess that works."
"Christian Bible, the Gospel of Mark, chapter five, verse nine." The newly named Legion recited. "We acknowledge this as an appropriate metaphor. We are Legion, a terminal of the Geth. We will integrate into Normandy."
"Hold it right there!" Commander Shepard ordered, storming into the AI core. "Doctor, what the hell were you thinking!?"
"Well, it helped us back on the Reaper, so..." The Doctor sheepishly shrugged.
"Do you have any idea what could've happened!?" The Commander scowled.
"You were going to reactivate it anyway." The Doctor reminded her.
"Yes, but I was going to go that after I put a security detail in here!"
"Oh... I messed up, didn't I?"
"A bit, yes." Shepard responded. She rubbed her temples, and said; "Alright, Legion, you aren't hostile, right?"
"Good." The Commander nodded. She brought up her omni-tool, and deactivated the kinetic barrier. "Welcome aboard." She welcomed, holding out her hand.
Legion looked down at the extended hand, and took it, shaking it. "We anticipate exchange of data."
"Oh, well, good!" The Doctor clasped his hands together. "That went as well as it possibly could've!"
"Given the circumstances, yes. But you really shouldn't have reactivated Legion without telling me!"
"How do you know his name's Legion?"
"EDI streamed the security feed live to my omni-tool."
"...Et tu, EDI?" Was all the Doctor could say.
"Do we really have to do this?" River groaned, as the Doctor led her out of the TARDIS, and up to the CIC.
"Yeah, a bit. Imagine if Shepard found someone new roaming around on the ship without warning. She'd think we'd been boarded!" The Doctor explained, pulling her into the elevator. "Plus, future her said we did, and I'd rather not have time rip apart. You understand."
"It's just that she's so... infuriating." River answered, clenching and shaking her fists. "So smug, cold, self-absorbed..."
"Obviously, you and I know two different Shepards." The Doctor remarked. "Just relax. It won't take long, and afterwards, we can go do whatever you like."
"Can we rob a bank on the Citadel?"
"No! ...Well, it depends. If people are in danger by not robbing it, then sure." The Time lord answered, the elevator coming to a stop on Deck Two. The door slid open, allowing them to step out. Shepard herself was overlooking the Galaxy Map and frowning at something. "Shepard."
"Doctor." She responded, turning around. Her eyebrows raised once her eyes came to rest on River. "River?"
"Yes." The Doctor answered. Shepard was about to open her mouth again, but the Doctor beat her to the punch. "But she doesn't exactly remember you. Well, it's more like she hasn't met you at all yet."
"...More time travel stuff?"
"Bingo! This," The Time Lord gestured to River, who was standing a bit awkwardly to the side, "River, is freshly-regenerated!"
"Ah, got it." She nodded. "So, how'd it happen?"
The Doctor looked affronted. "Shepard, you can't just ask that!"
"...Let's just say, she's from the future."
"Right, the whole 'you should never know your own future' thing. Glad I watched Back to the Future." Shepard said, then she addressed River. "Welcome aboard, I suppose. If you need something to do I'm sure one of the crew members can help you out." Then, she turned back to the Galaxy map.
"...What are you doing?" The Doctor curiously inquired, looking at the Galaxy map.
"After you left the AI core, I talked to Legion myself. It said there was a station filled with Heretic Geth with a virus that could turn all Geth over to their way of thinking. Into believing that serving the Reapers was the best thing to do."
The Doctor's eyebrows raised sharply. "That isn't good."
"No, it's not." Shepard deadpanned. "I'm just pouring over the navigational data one last time. We're going to have to take the shuttle because of the IFF installation, so I want to make sure we won't be detected."
"Commander, the course is sound." EDI piped up. "There is a ninety-nine point three percent chance you won't be detected by Geth sensors."
"Ah, so I'm just being paranoid then. Well then, notify the team." Shepard ordered, stepping down from the Galaxy map, and into the armory. "I'll take who I want with me when we get closer to the objective. That means you have to come too, Doctor."
"Well, duty calls." The Doctor responded, following the Commander. "...I have a duty now?"
"I'm coming too." River said, following along.
"River-" The Doctor began, but was cut off by River holding her hand up.
"I've been waiting to get out and shoot something since I regenerated."
The Doctor turned to Shepard, causing the Commander to shrug in response. "As long as she can fight, it's fine by me."
"Oh, I can fight." River chuckled.
The door to the armory slid open, and Shepard walked inside, retrieving her armor from the locker. She suited up, and picked the weapons she wanted to take. She handed River a spare kinetic barrier generator, a shotgun, and a pistol, and Shepard led them back over to the elevator. They all stepped in, and Shepard hit the button to take them down to the shuttlebay, where the team was already waiting. Shepard gave the order to board the shuttle, and the team did just that.
The shuttle door swung closed, and the Normandy's shuttle bay door opened up. The shuttle lifted off the deck, and shot out of the bay, jumping to FTL towards its destination.
Meanwhile, a few decks above, Susan was assisting Doctor Chakwas in doing more bloodwork, with samples taken from Shepard and sneakily taken from the Doctor.
"Amazing..." Doctor Chakwas breathed, looking through a microscope at the sample. "I dosed these samples with enough radiation to kill someone stone-dead in five seconds. But it looks like they weren't exposed at all!"
"In Gallifrey's early history, something happened that caused our ozone layer to be stripped away." Susan began to explain. "Without it, we were much more susceptible to UV and cosmic rays, so we adapted."
"Well then, your species is remarkably well-adapted! You'd give the Krogan a run for their money in the resiliency department. Imagine what could be cured if we could somehow adapt the Regeneration process to work for all species..."
"Theoretically, anything." Was Susan's response. "As long as it didn't kill too fast. But then we'd have to expose everyone to the time vortex, and-" As Susan was in the middle of speaking, alarms started blaring, and red lights started flashing. Susan didn't know what the alarms were signaling, but it seemed that Doc Chakwas did.
"It's the intruder alert, we're being boarded!"
"Boarded!? By who?"
Just then, EDI gave an announcement over the ship's announcement system. "Attention, all hands, the Normandy has been boarded by the Collectors. All hands prepare to repel boarders."
Susan looked outside the sickbay's window, and saw the crew frantically grabbing weapons, and rushing to combat positions, but not all of the crew, it seemed. Susan, thinking fast, grabbed her own sonic screwdriver out of her pockets, and rushed out of the sickbay.
"Ms Chambers!" Susan ran up to the Yeoman. "You and the others without weapons have to get out of here!"
"But there's nowhere to hide!" Kelly rightly pointed out.
Susan looked around for a moment, and saw the port observation deck. "In there, I'll seal the door behind you!" She ushered, as the elevator began to come down to their level from the CIC. It could have only been filled with one thing-the Collectors. "Hurry!"
Kelly, along the others that didn't have weapons or just couldn't fight, was pushed into the observation deck. The door closed behind them, and Susan deadlocked it with the sonic screwdriver. It was then that she turned around, and saw Joker run out from Life Support Control, and across the deck, intent on making it into the sickbay for some reason.
Susan, deducing that he had a plan, ran to follow him, but as she turned the corner, a Scion grabbed her, making her drop the sonic screwdriver, her only means of defense against the hulking creature. Susan yelled out, shouting for help as the Scion pulled her into the elevator, and it and the other Collectors forced her into one of the pods they used. The pod sealed around her, and in moments, Susan lost consciousness...
Back on the shuttle, several minutes later, the shuttle's comm beeped, notifying them all of an incoming message. Shepard got up, and walked over to the comm panel, pressing the button to answer it. The message was text-only, and very short, but that didn't lessen the impact it had.
Shepard peeking into the shuttle's cockpit. "Pilot, turn this thing around!"
"Ma'am?" Was the pilot's confused response.
"The Normandy's been attacked by the Collectors! Get us back to the ship now!"
"Aye, aye!" The pilot responded, turning the shuttle around, back on course for the ship.
On the entire ride back, the unrest and unease in the shuttle was almost palpable. About fifteen minutes later, the shuttle finally rendezvoused with the Normandy, and landed in the shuttle bay. The shuttle had barely landed, before the door opened, and the Doctor rushed out, frantically searching around for Susan.
"Susan!?" The old grandfather fearfully yelled, hoping beyond hope for a response. He took the sonic screwdriver out of his pocket, and set it to track Susan's. The device gave off a deep whirr which heightened in tone and pitch as he pointed it upwards, towards the upper decks. He ran into the elevator, and pressed the button to take him up. He went up a deck again once he realized that the other sonic was still above.
The elevator stopped on the crew deck, and the Doctor rushed out, following the sonic's change in sound to the other device. Eventually it led him right outside the med bay's door, upon whence he looked down, and fell to his knees.
His hand shook as he reached out and picked up Susan's sonic screwdriver, still warm from being held in her palm.
As Shepard walked up behind him, and tried to console him, the Doctor wanted to cry...
But all he felt was rage. Rage that some cruel force in the universe robbed him of a loved one. Rage that this had happened to him again. Rage that he let this happen to him again.
But most of all, a blinding, incomprehensible rage towards the Collectors.
He stood up, stashed both screwdrivers in his pockets, and stomped back to the TARDIS.
He'd get Susan back. But if the Collectors harmed her in any way...
They'd have Hell to pay.