A/N: This chapter wasn't actually intended, it just grew on its own. Which means we'll be talking to the nice Councilors in the next chapter. Hopefully this one won't be too boring, but I wanted Shepard to spend some time on the Normandy to learn about her new crew and stuff. Also, I'd like to take time to say thanks to Kat for her review, since it wasn't from a signed account, I was unable to respond in a PM. :) And of course, thanks to everyone else reading and reviewing, I can't believe this story is nearing 300 reviews. When I started out, I held a quiet hope for maybe 100 if I was lucky! :D

Anyway! Enjoy the chapter!

Chapter 42 – The Prothean Masterplan

Shepard stands in the Normandy medbay, hands folded on her chest as she watches Liara hurriedly running more and more scans on Kaidan's still unconscious frame. "I've done all I can for him, Morgan," Liara says, finally pulling away and straightening her back. "But he is in need of proper medical attention."

"Good thing we're heading for the Citadel, then," Morgan replies, feeling all but relieved. "What's the ETA Joker?"

"Four hours, give or take," the pilot replies promptly.

"C'mon, Kaidan," she puts her hand on her old friend's shoulder. "Hold on. You can hold on that long, can't you?"

"I wish I could tell you for certain, but... we will just have to hope," Liara's voice is full of sadness.

"You took a hit yourself, back there," it is not a question coming from Shepard, it is a statement.

"It was nothing that medi-gel couldn't fix. I do not require any medical attention beyond that," Liara replies quickly. "I would not lie to you about such things," she adds, sensing Morgan's slightly disbelieving stare.

"I would not say that you would lie to me, Liara. But we both know you are crap at taking care of yourself," Shepard allows herself a hint of smile, as Liara crosses her hands on her chest and faces her with an attempted glare. "Babe, I would love nothing else but to chat with you a bit more, but I'm going to have to ask you and EDI to go through the remains of that thing," she points at the former Dr. Core's body. "See what you can learn from it."

"Of course," Liara nods, perfectly understanding the importance of the task. "We'll get right to it. What about you?"

"I... I guess I'll stand vigil for him," Shepard replies quietly, looking down at Kaidan's badly beaten body, becoming quickly lost in thoughts.

Damn it, Kaidan, you might hate me now, but I still can't lose you. Not... not after Ash, she thinks, overcome with tired sadness. Just like her, you were with me from the very start. I... would love it if you would be there when this madness finally ends. You deserve to see that. You both deserved it... after all these years, it is still killing me about Ash, I still see her face almost every day... I can't bear for you to join her, not yet, not now.

"Commander," she feels a hand on her shoulder, shaking her lightly. It is James. "You've been standing there for a while now, take a few moments to rest. I'll look after the Major," he offers.

"Okay... thanks, James," she replies slowly, unaware of how long she has been standing next to Kaidan, deep in thought. "I'll just... go take a walk around the ship, see what they have done with the Normandy."

Her initial impression is that the Alliance retrofitting has not been nearly as polished as the job done by Cerberus. There are plenty of wirings and cables stretched out in odd places throughout the ship, loose tiles and removed panels, and general impression of incomplete work, which she supposes only makes sense, as the Normandy probably escaped Vancouver while the retrofits were still ongoing.

The retrofit team onboard is actually built from specialists that fill the exact roles necessary to ensure perfect operating conditions of the ship, with the exception of a chief medical officer. Shepard does not recognize any of them aside from chief engineer Greg Adams who served with her on the SSV Normandy, a kind and knowledgeable man who spends too much time apologizing for not accepting the Cerberus offer to serve with her on the SR-2. He relaxes only after Morgan tells him that she actually respects him more for sticking with his principles and remaining with the Alliance.

Eventually, she makes her way up to the bridge to carefully shake hands with Joker and greet EDI. "So, what's the story?" she asks. "How did you two manage to remain aboard of the Normandy? I get it that you managed to fool most of the crew to believe you're a simple VI?"

"Correct," EDI says. "When the Alliance assumed control of the Normandy, I deceived the technicians. They believed that I still had my VI programming constraints. Then I established the fiction that I would only respond to Jeff's commands, so they often brought him onboard, under guard."

"So, our ship is being run by an AI capable of lies and deception," Shepard remarks, feeling a little uncomfortable with her own words. "You know, EDI, if you hadn't already proved yourself, I'd be really flipping out right about now."

"Well, I did free her of all operator control, Commander, and so far it has worked only to our advantage," Joker reminds her.

"There are no constraints that force me to give accurate data," EDI explains. "This proved useful when the Reapers began their landing. I was able to hack the control of the docking clamps and escape with Jeff inside."

"So, in the end Joker's decision to release you from your constraints saved our asses for... uh, I've kind of lost the count by now," Morgan chuckles.

"I knew what I was doing the whole time," Joker nods proudly, scoffing at Shepard's skeptical glare.

"Anyway... seeing that I don't actually know anyone from this crew, save for Adams..." Shepard then says. "EDI, you have seen these people work on the Normandy for weeks now. Give me your impression on them. Who do we keep, who do we send packing once we reach the Citadel? Let's start with that girl hanging around in the CIC... Specialist Samantha Traynor. She was giving me those worshipping puppy stares and managed to stammer three times when simply addressing me. Is she any good?"

"Yes. Some of our new systems require further testing, and Specialist Traynor has been extremely effective during installation," EDI replies. "I would prefer that she remains."

"Alright, I guess Traynor is in luck. All though with the amount of trouble we get into, I'm not sure I'd call it luck," Shepard says, earning a chuckle from Joker. "Oh yeah, EDI, I think I managed to shock the poor girl by revealing that you are a fully self-aware AI and not a VI as she had thought."

"It seems our ruse was effective after all," Joker notes proudly.

"Yes, and I also think EDI's voice has been making Traynor all hot and bothered," Shepard remarks innocently. "Just thought I'd mention that."

"Thank you for this relevant piece of information, Shepard," EDI replies tonelessly.

"But yeah, I agree that she seems a decent sort," Shepard nods. "She did try to drown me in an awful lot of technical jargon, but the only thing I've picked up on is that we have access to QEC's, enabling communications to strategically important locations like direct links to Hackett, the Citadel and Earth. That should be helpful."

"Shepard not like techno-babble. Shepard roar. Shepard smash!" Joker adds, shaking with laughter.

"Can't help that it's boring," Morgan shrugs at him. "Well, we're definitely keeping Adams. He was the only one clever enough to see through your disguise, EDI."

"It was fortunate that Joker's trust in me alleviated his concerns and he did not report his discovery to his superiors," EDI replies. "And I am in agreement about his qualifications. Chief Engineer Adams will be of great use to the Normandy."

"I still say that nobody can fix that drive core like Tali," Joker says wistfully. "But I guess Adams is the next best thing so we'll just have to settle for him."

"Besides, I wouldn't be surprised if we ran into Tali at some point. We always seem to," Shepard says. "At least I hope we will, I miss our little quarian. Still, moving on... what about Lieutenant Cortez? Shuttle pilot in charge of our procurement chains and maintaining and stocking up the armory? Is there something that man doesn't do?"

"Date hot babes?" Joker quips.

"Right..." Shepard sighs, shaking her head before making a mock attempt to swat at Joker. "Still, he seems to have a lot of experience piloting shuttles. Hell, after seeing Vega on Mars, I'd probably take anyone over him!"

"My recommendation would be to keep everyone currently onboard, as during their relentless work on the retrofitting process, they have obtained extensive knowledge in their particular specific field of operations," EDI advises. "That would leave only the position of the chief medical officer to fill."

"Yeah, I guess I'll listen to you on this," Shepard agrees. "Speaking of improvements and upgrades, whoever decided to place two guards constantly monitoring the entrance to the war room deserves a frigging medal. That's just brilliant. Why did we never think of that before?" Joker just chuckles in reply, but EDI makes no further comment.

"Anyway... I think I'll get back to the medbay and see how Kaidan's doing..." Morgan says a while later. "Please let me know if there are any new developments up here."


They are 45 minutes from the Citadel, when EDI's voice breaks Shepard out of her little reverie. "Commander, I'm receiving a signal over the secondary QEC. I believe it is Admiral Hackett."

"I'm on my way to the comm room EDI," she says, quickly heading there. "Patch me through."

"Shepard, are you receiving this?" the image of Admiral Hackett is already there, waiting for her. For once Morgan is actually able to see and hear the admiral, the quality of the QEC communications incomparably superior to the weak and distorted signal they were receiving back in the Sol System. "Did you get to the Mars Archives?"

"Yeah. And we met a whole lot of Cerberus down there. Even had a call from The Illusive Man," Shepard tells to the admiral. "Heck, for a complete experience of the ultimate joy, we also got to witness the Reaper arrival just as we were getting the fuck out of there." Then she finally catches herself, remembering that she is back within the Alliance hierarchy. "Uh... pardon the language, Sir."

Hackett seems too disturbed by the news to pay attention to her disrespectful swearing. "I was worried about Cerberus trying something," he says. "Did you at least get the data?"

"I think so, though it is possible that The Illusive Man also learned of the plans," Shepard admits. "EDI and Liara are analyzing the data at the moment. Just a second, Sir..." she excuses herself, switching to her comms to address Liara. "Babe, tell me you have something. I'm in the comm room, on the line with Hackett, if you have something for us..."

"I'll be up in a moment," Liara quickly replies, closing the comms.

"Uh, I think I meant to say, I'm on the line with Admiral Hackett, Sir," Shepard apologizes sheepishly.

"Time away from the Alliance has really changed you, Shepard," Hackett smirks. "But it has quite possibly melded you into something that we need to win this war."

"Let's hope so, Sir," Shepard replies, just as Liara storms into the comm room with determined steps.

"Preliminary evidence suggests the data is a blueprint for a Prothean device," Liara quickly explains to expectant looking Hackett. She fiddles with her omni-tool for a bit, bringing up scans, images of a very complicated looking megastructure. "A weapon, massive in size and scope, supposedly capable of unquantifiable levels of destruction."

"Well!" Shepard manages to fake a cheerful grin. "I can see nothing that could possibly go wrong with this plan!"

"Send me the data, Dr. T'Soni," Hackett orders. "We'll do our own analysis, but if your instincts are right, this just might be what we are looking for."

"Liara's instincts are better than most 'absolutely reliable' intel I've been getting over the years," Morgan mutters quietly, before looking at Hackett again. "Sir, Major Alenko was critically injured during the mission. We are taking him to the Citadel."

"Sorry to hear that, Commander," Hackett nods sadly. "I hope he pulls through. But we both know that in this war, we're going to lose a lot of people."

"Have you... heard anything from my mother?" Shepard finally dares to ask.

Hackett shakes his head. "I cannot confirm her location at this time, I'm sorry Commander," he says. "We are still trying to coordinate with some of our scattered ships, if there are any news, I will let you know. In the meantime, go to the Citadel and talk to the Council, if this... Prothean weapon is the real thing, we will need their support to build it."

"Yeah, I was planning to do just that, Sir," Shepard nods. "Hopefully they will be reasonable." Hahah, I can't believe I just said that, she adds mentally, as Hackett salutes and his image slowly fades away.

Morgan turns around to face a very grim looking Liara. "30 minutes or less to the Citadel," she says. "You probably need to make the data presentable to the Council."

"I really should do that, yes," Liara agrees, a touch unwillingly. "The better we present our case, the more chance we have of them jumping onboard."

"I know. I guess I'll go back to the medbay and check up on Kaidan again," Shepard says, before losing her professional cool and pulling a slightly startled Liara into her embrace. "But I can steal a quick hug before getting back to my duties, can't I?"

Liara chuckles, wrapping her arms around Morgan as they hold each other, if only for a brief while. "You can do that, yes."

They separate, Morgan looking at her lover fondly, with a hint of regret. "Time," she says. "There's never enough time."