PROLOGUE

Partial Transcript of Interrogation of S. Shepard (former Alliance Cmdr.)

Alliance Earth Command

March 3, 2186

Col. Skinner: "And you can't name one person to corroborate your story."

Shepard: "I can but I won't. They risked their lives by following me to stop the Collectors. They all deserve medals for that but you'll throw them in prison for it. I did you a favor by turning myself in. I won't betray my crew though."

Col. Skinner: "So now you're protecting known criminals, mercenaries, and terrorists?"

Shepard: "I'm sure Cerberus has people like that working for them but I trust my crew Sir."

Col. Skinner: "I still don't understand Shepard. Up until just recently your record was spotless and you were one of our best. You always put your duty first and worked by-the-book: You showed exemplary courage and leadership on Elysium, became the first human to earn a position with the SPECTRES, and in that spot you managed to keep Alliance interests at heart and still stay on friendly terms with the Council. You didn't seem anti-alien at all like other Alliance soldiers do: you gave the order to save the Council during the Battle of the Citadel despite the human cost. Do you regret that? Is that why you faked your own death and joined up with Cerberus?"

Shepard: "I didn't fake my own death. I died."

Col. Skinner: "Of course you did. And Cerberus 'resurrected you to be humanity's savior.' I still think you just lost it: all that talk of ancient sentient starships coming to kill everyone didn't help your reputation even before this business with you and Cerberus."

Shepard: "The Reapers are real. Your own fleets fought against one three years ago and saw how powerful it was. And 'this business with Cerberus' has nothing to do with why I'm here. That mission to the Bahak system was a favor for the Alliance, because they didn't want to take responsibility for it. The plan to destroy the Alpha Relay was orchestrated by an Alliance operative, and it was to delay the Reapers. I'm just the one that pushed the button."

Col. Skinner: "If that was an Alliance facility then where is the crew? Dr. Kenson? You killed them all and then murdered 300,000 batarians. I know you're probably still angry about Mindoir, your family, but good God Shepard I thought you got your revenge in the Blitz, not like this."

Shepard: "Admiral Hackett saw the report and debriefed me in person. Why don't you take it up with him?"

Col. Skinner: "Believe me, I have. He may support you and your story, but he is clearly not an impartial party and is not on this judiciary board. His testimony will be acknowledged in our final review. I can see you won't cooperate, so if that's all we'll just end this interrogation early and we'll look over the reports with the judiciary…."

Lt. Col. Scully: "If it's all right Sir, I'd like to ask Shepard a few questions about the aliens he claims to have fought, the Collectors."

Col. Skinner: "Go ahead."

Lt. Col. Scully: "We have had limited reports about them, including one filed by Maj. Kaiden Alenko about your encounter on Horizon. If they really did have technological capabilities as advanced as he and you yourself described then how did you defeat them?"

Shepard: "A little luck and a lot of help from the best damn squad in the galaxy. Obtaining an IFF to navigate the Omega-4 Relay also gave us an advantage. The Collectors were hit-and-run attackers; they weren't prepared for a stand-up fight with their backs to the wall. This is all in my written statement and interview notes…"

Lt. Col. Scully: "Yes, I know. And I understand how a strike team could hold their own against them on foot, but you claim to have destroyed them completely. How did you take out a Base that size with just the Normandy's armaments?"

Shepard: "The station controls could be sabotaged to overload critical functions and destroy the base. It was just a matter of getting there."

Lt. Col. Scully: "So that's how you destroyed the base?"

Shepard: "Sir, Ma'am, I believe I've answered all of these questions many times now. You have my story: it's the truth and I'm sticking to it. I'll let you make your decision now."

Lt. Col. Scully: "But nowhere in these logs do you discuss destroying the Collector Base. You say you traversed the Omega-4 Relay and defeated the Collectors and the 'Human-Reaper' they were building. But that's it. Tell me, what happened to the base?"

Shepard: "You're the only who seems to notice that I've been dodging that question. I used the station's controls to deliver a radiation pulse to kill everything on board but keep the base intact."

Lt. Col. Scully: "I don't understand…"

Shepard: "The technology there could help us fight the Reapers. Despite the horrors there, I couldn't just throw it away."

Col. Skinner: "You handed it to Cerberus, didn't you? Collector tech, Shepard? Are you out of your damn mind? Do you have any idea what kind of damage they could do against us, against our allies with that stuff?"

Shepard: "Yes, but think of what it could do against the Reapers as well. We're going to need every advantage we can get to even have a chance at stopping them."

Col. Skinner: "If they even exist! You gave a known terrorist organization some major technological upgrades to fight an imaginary enemy. What if there are no Reapers? Cerberus could use that technology against the Alliance and the people that die when that happens will be on your hands!"

Lt. Col Scully: "Colonel, we need to share this new development with the rest of Command right away."

Col. Skinner: "(into the radio) Lt. Vega, please escort Shepard back to his room. I want guards posted round the clock, and no visitors. No exceptions."

CHAPTER 1: THE CALM BEFORE

"…just enjoying the calm before the shit-storm, Commander."

– Flight Lieutenant Jeff "Joker" Moreau

Normandy Bridge listening device recording

Logged by Enhanced Defense Intelligence (EDI)

Six Months Ago

"This is bullshit, Commander! The Alliance looked the other way this whole time you've been working with Cerberus and now they want to lock you up for doing their dirty work? Fuck 'em. This is a stealth ship, it's not like they can catch you."

"I never thought I'd say this, but Jack's right. You can't afford to waste your time in a prison cell waiting for a show trial, not with Reapers inbound. The galaxy needs you here...I need you here."

"I'm sorry Miranda. I have to do this. We need the Alliance to be ready for the Reapers. Cerberus may be the only ones doing anything about it now but they're not an army. Their size and resources were enough to take down the Collectors, but it won't be enough against the Reapers. We need an army. We need a fleet. Cerberus has 150 operatives and spent most of its resources on me and this ship. The Alliance has millions of soldiers and several fleets. We need them on our side."

"This is bigger than the Alliance. The Reapers are coming for all us, not just humans. I'll see if I can convince the Migrant Fleet to help too. They were already preparing for war against the Geth. I know that's wrong, but at least they'll be ready for heavy fighting if the Reapers get here. I'm still a candidate for the Admiralty Board, so I need to return to them. I'll do what I can to make sure they save their resources for the real war. I don't want to abandon my crewmates here though..."

"Don't worry about it Tali, you'll help more with your position in the Migrant Fleet. All of you just followed me on a suicide mission. I won't ask you to do it again, and I know some of you have other obligations: family, fleet, clan. The Collector Base mission is over. You're all free to go if you choose. You don't owe me anything; I owe you everything. The Normandy is yours now. Take care of her."

Normandy Crew Deck Lounge

Present

Garrus Vakarian gazed out across the stars through Normandy's port side window as he drank a dextro-beer. Another slow day on the Normandy, as usual. As the new Shadow Broker, Liara occasionally had some intel for them to follow up on but so far it was mostly dead ends. Most days were spent like this one: monitoring the general galactic news as well as more covert information channels with Liara's help for any sign of the Reapers but finding nothing. It didn't seem right to him. There should be so much more to do with Reapers on the way. But the Reapers weren't something a rogue vigilante and a handful of fighters could take on alone. He began to think maybe some of the others were right to leave, at least most of them were doing something productive:

Shepard was taking one for the team for the Alliance while trying to convince them to prepare for the Reapers.

Tali was now helping to lead the quarians as an Admiral, the highest-ranking position in the galaxy's largest fleet, trying to convince them to see the truth about what was coming and to try and make peace with the Geth. She was in contact with Legion about this while 'they' were off exchanging data with the rest of the Geth and the re-formed Heretics to form a consensus about this same possibility, as well as what to do about the 'Old Machines'.

Urdnot Wrex was still leading the Krogan and trying to reform them for the better. Grunt was already leading his own squad of Clan Urdnot, spreading the word about battles to come and coordinating with Wrex about how to fight them. And Mordin was back with the STG but secretly working on cure for the genophage based on his former student's research he recovered on Tuchanka.

"And here I am sitting on my ass and drinking beer," Garrus thought. But someone had to hold the fort with Shepard gone. And he figured there would be no down time for anyone when the Reapers arrived, so they might as well enjoy it while it lasted. He just wished the rest of the gang was there too.

"Any news, Sir," Jacob said as he walked in.

"How many times do I have to tell you not to call me that?" Garrus responded. "I'm not the Commander. This is his ship. I'm just watching it for him."

EDI appeared as a blue hologram on a console in the lounge and chimed in. "Both Commander Shepard and executive officer Lawson were very clear that you are to be in charge of the Normandy."

He remembered, and it had taken him somewhat by surprise when it happened. He knew he was going to stay but he did not expect to be given command.

"Why couldn't Miranda just take over? She seemed fine ordering us around before some of us even trusted her. She's used to this job."

"So are you," said Jacob, "you lead a squad of vigilantes with no organized support that managed to drop Omega's crime rate single handedly."

"I got them all killed," Garrus replied grimly.

"It wasn't your fault," Jacob countered, "and when you found the guy responsible you spared him. You saw the bigger picture, beyond just revenge. That's the mark of a good leader. Look at Zaeed and what he tried to pull on Zorya. You're better than that. Give yourself more credit. Hell, I don't think we would have survived that little diversion at the Collector Base if you hadn't been leading us."

"Thanks Jacob," Garrus replied, "but I'm sure we'd have done just as well with you in charge, better maybe. Can I get you a drink?"

"Sure, sounds good," said Jacob as he sat down at the small bar next to Garrus.

"You guys sure have been tearing through all the human beers," Garrus joked. "We're almost out."

"Yeah, I guess you're well-stocked though," Jacob said. "With Tali gone, you've got the dextro-beer all to yourself. Then again, I can't imagine her drinking too much anyway."

Garrus laughed and said, "Don't let her bubbly little girl act fool you. Tali has more responsibility to deal with than any of us did at her age. Sure we've both commanded troops before in the military but we were only responsible for a small squad at most and there were always plenty of people higher up the chain of command. Now she's at the top of it. She's an Admiral responsible for her entire race."

"Can't imagine that..." said Jacob.

"She wasn't even considered a full adult when she joined Shepard to help stop Saren," Garrus said. "Then she joined up with us again to fight the Collectors. She's seen more action than most ever do and she's got some great stories, especially after a few beers have made her more talkative. She's a good drinking buddy."

"You two must be pretty close, after everything you've been through together," said Jacob.

"Yeah," Garrus replied. "She's a good friend..."

Admiralty Board Meeting Transcript

Migrant Fleet Diplomatic Envoy

Dholen System, Far Rim

Adm. Koris: "This war you've been advocating will be costly, and it may pointless. It is only a means to an end: what we really want is our homeworld back. If we can do the same through peaceful negotiations, as Tali'Zorah says we can, then there should be no discussion of-"

Adm. Han'Garrel: "And what if negotiations don't work? Even if this 'Legion' was telling the truth, which is a big 'if', it's only one Geth. Tali, you yourself claimed that the Geth are divided, and that your 'friend' was a special unit. What if it's the minority, or one-of-a-kind? Even "Legion' claimed that the Geth have no government or leadership, so how can we trust that this one speaks for all of them?"

Adm. Zorah: "Legion is a platform comprised of thousands of Geth, not an individual. And the Geth are no longer divided: Shepard and I assisted Legion in re-writing the Heretics to fall in line with the true Geth. The Heretics were trying to do just the opposite. We were lucky we met Legion when we did, otherwise the Geth would be united against us."

Adm. Daro'Xen: "Re-written? So the Geth can be hacked...interesting. If we could get our hands on that program-"

Adm. Zorah: "Legion deleted it after we used it, with good reason. We couldn't risk it falling into the wrong hands. If the Heretics tried to use it again-"

Adm. Han'Gerrel: "So you and the Geth are 'we' now? Have you forgotten what those things did to us? What they-"

Adm. Koris: "Only because our side struck first, which you are planning to do again at this very moment. Our history will just keep repeating itself unless we can break this cycle."

Adm. Han'Gerrel: "By making nice with those 'things' that drove us from our homeworld, and continued to fight us for the past fight 300 hundred years? They are a mistake we must erase, and I-"

Adm. Daro'Xen: "Or correct. If they can be re-written then we could make them serve us once more. Imagine what a synthetic army like that at our command could do for our people. The Council would have to stop treating us like second-class citizens if we had the power to-"

Adm. Zorah: "The Geth are sentient, they're not just machines. They're just misunderstood. And we don't need to hack them to get them on our side. We can convince them to join forces with us of their own free will to help fight the Reapers-"

Adm. Daro'Xen: "Machines don't have free will, Tali."

Adm. Han'Gerrel: "And this Reaper nonsense again? This discussion is about the fate of our people and re-taking Rannoch, not some Prothean legend you and Commander Shepard believe in."

Adm. Koris: "Reapers or not, we need to be negotiating with Geth about returning to our planet, not starting another war over it. War would result in untold casualties and leave us vulnerable to any threat."

Adm. Shila'Raan: "(entering the room) Admirals, I'm afraid this meeting must be adjourned immediately. There is some troubling news you need to see..."

Salarian Special Tasks Group Facility 52

Sur'Kesh

Location Classified

Mordin Solus was interrupted from his laboratory work by the Salarian dalatrass via hologram. "It is fortunate that you were able to put a stop to Maelon's research, Professor," she said. "You were very discreet, and the Krogan are none the wiser. This data, or even just knowledge of it, could have started a major galactic incident like another Krogan Rebellion. You have my personal thanks for your handling of the situation."

"Gratitude appreciated, dalatrass," Mordin replied. "Know you're very busy, took time to deliver thanks personally, honored."

"I hear you've been quite busy as well, Professor," said the dalatrass. "The STG could use more brilliant minds like you. I'll let you get back to work." She signed off.

Mordin returned to his lab bench and continued the day's experiments, but the dalatrass's words troubled him. He had stopped Maelon's research because his methods were monstrous, not to keep the Krogan down he told himself. But he knew that wasn't true: his life's work, the modified genophage, ensured the Krogan infant mortality rate would remain 99.9%. At the time he had thought it was necessary, the only option that would not lead to war. But with Urdnot Wrex leading his people the Krogan were making positive changes, showing that they could be more than just mercenaries, brutes, aggressors.

Mordin believed that a culture should advance at its own natural pace and that 'shortcuts' or technologically uplifting a culture before it was ready could be disastrous. The Salarians uplifting the Krogan to fight the Rachni is what led to the Krogan Rebellions and necessity of the genophage in the first place. But was the reverse true for cultural advancement? After a thousand years Krogan physiology was starting to adapt to the genophage and overcome it. Naturally. Then he had engineered a new modified genophage to undo the adaptation. Was artificially stopping a civilization's natural development just as bad as accelerating it?... Wasn't that what the Reapers did?

The dalatrass was right about one thing though, he thought. If the Krogan found out that research close to curing the genophage had been taken right out from under them on Tuchanka things would be...problematic. Deleting the data would have been much better for security, and is what his old self might have done, but Mordin's experiences serving with Shepard on the Normandy had changed him. He regretted what he had done to the Krogan and saw it as a wrong to set right before he died. And Maelon's work was a huge step forward for that, even if his methods had been brutal. Mordin felt partially responsible for Maelon's victims as well, and thought that using the data for a good cause would at least mean their deaths meant something. But he still didn't have a cure. He was working on one in secret, claiming that he was working on preventing cure attempts like Maelon's, but was still some time away from finishing it. If the Krogan got word of this they would want it. Immediately. Maybe even go to war for it. So for now, he had to keep it quiet.

Normandy Crew Deck Lounge

Present

The lounge door opened and Miranda walked in. "Having a little guys' night and drinking on the job? I'm disappointed," she said. "

"Wha-?" Garrus started.

"-Disappointed that you didn't include Joker," Miranda continued. "I think he gets lonely up on the bridge, especially with the ship so empty as it is."

"You care about all of us now?" Garrus joked.

"I've always cared about this crew's safety and well-being," Miranda responded, "Couldn't survive a successful Collector Base assault without a full squad focused on the task. But we've been through a lot together and it's more than that now. You know that up until recently I had no family to speak of and well...I think all of us make a sort of family together. A good one."

"Likewise Miranda," Garrus replied happily, "I never pictured this happening back when we first met, but I'm glad you're here. And I'm sorry if I crossed any lines teasing you and Shepard. You two are great together and I didn't mean anything by it."

"It's fine Garrus," Miranda replied with a smile, "I did need to lighten up before, and I'm sorry if I was too abrasive at first."

Then Jacob said, "it's nice to have some time together like this, and I think you were right about including Joker, Miranda. I say we take this party to the bridge."

As he said this, Kasumi Goto entered the room. "A party huh? Count me in", she said.

EDI appeared again to say "Alcohol consumption outside of designated areas and while on duty is against ship regulations..." After getting confused looks she continued, "that is a joke."

Shadow Broker Base Ship

Hagalaz

Liara T'Soni was frantically trying to process all the new information that had suddenly started coming into her office. As the Shadow Broker, her sources were usually faster than normal channels, but whatever this was wouldn't stay secret for long. Something big was happening. And based on the reports coming in, it didn't look good.