This is the first chapter in my new story covering the interim from Mass Effect 2 to Mass Effect 3. For exposition on the characters read this:
Commander John Shepard-A paragon Spectre who grew up on spaceships and endured fighting batarians on both Elysium and Torfan. He has begun to break under the pressure of all that has happened, and the horrors he has seen Cerberus commit, letting his ruthless demeanor break through his kindness.
Cynthia Shepard-John's clone created by Cerberus, she loyally followed him on the hunt for the Collectors, slowly growing an affinity for Garrus that led to their budding romance. She and Shepard broke into the C-Sec headquarters and created a civilian profile for her as one of Shepard's cousins.
No one died on the suicide mission, all loyalty missions went well, Wrex is alive, etc.
Currently, the only ones on the Normandy are Shepard, Cynthia, Tali, Garrus, Miranda, Jacob, Chakwas, Joker, and EDI. The rest left after the Collector mission to return to their respective lives and help prepare for the Reapers, but Chakwas stayed for Joker, and Miranda and Jacob would be hunted down for defecting from Cerberus if they left.
Shepard stared at Tali with dead eyes as she recoiled from his words.
"What do you mean you have to go? I still don't know what happened down there!"
Shepard sat down at the foot of the bed and began to explain. Through the mask he could see her face contorting in pain and anger as she realized the full implications of what had happened.
"John, you can't just turn yourself in, you have to fight this!"
Shepard croaked out dejectedly, "I can't win this. Harbinger indoctrinated Kenson and lured me there, knowing he would win no matter what happened."
She slapped him as tears coalesced in her eyes, her anguished words turning to yelling, "You have to try! I already lost you once-I'm not going to let you go again!"
Shepard shook his head, "I can't go on the run from the Alliance. I wouldn't make it."
Tali's anger turned to sobs as she clung to him, "You-you can't just leave!"
After an hour or two like that she fell asleep in his arms. He lay her down on the bed and walked down to the mess hall, greeting Cynthia and Garrus for a late-night drink.
"Spirits, Shepard what happened in the Bahak system... I couldn't have made that call. I want you to know I think I did the right thing."
Shepard silently took his seat. "I just wanted to let you know I'm taking you two to Palaven before I go to Earth. It wouldn't be good for you to be found in my company when they seize the Normandy."
Cynthia's eyes darted to Garrus, "Actually we've been talking about that. Hackett emailed me with a proposal and I took it. I'm getting a post in the Alliance. On Earth, actually. First person to ever start as a captain."
Despite the circumstances, that peaked Shepard's interest, "Captain? He'll do that? And what about you and Garrus."
The turian took a swig of turian brandy and responded, "I'm going back to Palaven, see what I can do with the Hierarchy to prepare for the invasion. As for us... well, long distance isn't that bad."
Cynthia grinned, "Our little 'incursion' at C-Sec headquarters didn't go unnoticed. Hackett covered it up and made it look real-apparantly just making me your cousin instead of your sister wasn't enough to stop alarm bells from going off. He falsified a military career. 'Can never have too many Shepards' he said."
Shepard let a faint grin cross his face for a second. Miranda stepped out of her office and glanced at the table, "Shepard, Cynthia, I need to talk to you."
They shrugged and followed her into her office.
Miranda sat down and gestured for the duo to do the same. As they got comfortable she took a deep breath. "I... I don't know how to say this, but I've gone over reports of the Lazarus Project. After you got back from Aratoht we ran tests and... and... Shepard, you're dying."
His face sunk and he rubbed a hand through his hair, "What?"
"Your replacement organs aren't working properly. We did the best we could in the Lazarus Project, but we-"
"How long?"
"..."
"How long Miranda?"
"Best estimates say you have maybe two years left. I'm sorry Shepard."
Cynthia leaned over and gave her brother a hug, "I... We're all here for you, Shepard. I-Jesus, that came out of nowhere."
Miranda nodded, "And this is comparatively better, but still, you might want to brace yourself. Both of you were rendered infertile by your respective... resurrection and creation.
Shepard and Cynthia glanced at each other. Cynthia was the first to speak, trying to break the tension, "Well with our choices in companionship, that shouldn't be too much trouble, right Shepard?"
The commander just slowly stood and left the room.
Liara T'Soni stood in her room on Hagalaz, going over the Normandy's video footage for the day. She had promised Shepard she would disable all of them when she became the Shadow Broker, but she just couldn't. When Shepard was going through something rough, she always just called him under the guise of checking up. He could clearly tell what was happening, but he hadn't said anything yet.
"Shepard is dying."
Miranda's voice stopped Liara's thoughts dead in their tracks. As she finished watching the video, she began to call Shepard."
Shepard walked into his cabin and sat at his desk. He looked through his messages and waited. Finally, the call came. "Liara."
"Heh, yeah. I just wanted to-"
"Cut the bullshit."
His harsh tone shocked her. "Are you okay, Shepard? I just heard."
He stared ahead for a few moments, not responding. Then a smile began to form on his face. "I need you to do something for me."
Tali awoke to find Shepard next to her. It was a welcome constant from what she had learned before she fell asleep. He was holding his omni-tool, taking a picture of himself.
"Keelah, Shepard what are you doing?"
He cheerfully handed her omni-tool over, "Giving you something to remember me by. I had a picture of you on the Normandy, it kept me sane."
He could see the faint outline of a smile. "I... thank you Shepard. And I understand what you have to do."
Shepard's lips pursed. "Yeah... Look, I'm going to drop you off at the Migrant Fleet. I've already secured everything."
In contrast to her previous attitude, she nodded. "I understand." Trailing her finger up his chest she added, "Maybe they'll allow conjugal visits."
Shepard laughed, "Miss vas Normandy, are you trying to get me into bed?"
"Desperately."
He grinned, "One for the road?"
Tali unclasped her mask, "One for the road."
Shepard waved goodbye to Tali. She was tearing up, but she hid it well. She was being strong for him.
Garrus and Cynthia stood next to him, waving as the airlock door closed. As it finished, the Normandy departed from the Neema, heading for the nearest way to Palaven.
Garrus' happy demeanor dropped, as did Shepard's "You didn't tell her, did you?"
"I'm not going to do that to her."
"She's an adult, she can take it."
"I love her, I'm not going to subject her to that kind of pain. Besides, it's better if she doesn't know. She'll worry less."
"And if you die again while you two are apart? She'll never be able to get past it."
Shepard turned to his turian ally and cracked a smile, "I don't intend to die just yet."
Garrus laughed and held out his arms. "I'll miss you, Shepard. Keep in touch."
"Whenever I can."
The two of them went back down to the mess hall. They were going to finish off whatever was left of the Normandy's alcohol supply before they had to turn it in.
Garrus stood in the cockpit of the Normandy, all his things gathered and packed away into a single box. "You ready, Cynthia?"
She wiped away a tear, "I... Yeah. You call me, okay? I don't want to find out that some scaly turian girl has stolen you away from me."
"That's not going to happen."
They embraced and shared a tender, passionate kiss. Garrus tried to open his mouth, but instead closed it and took off his eyepiece. He held it out for her. "Something to remember me by."
Cynthia smiled and looked at him, accepting it into her palm. She slowly put it on and leaned against him, taking a picture with her omni-tool. "I'll miss you Garrus."
"I'll miss you too. Don't get into too much trouble." Shepard and he had already said their goodbyes, so without anything else to help him linger there, he stepped out of the airlock and onto the docking port at Palaven.
The airlock closed and Cynthia sat down in the cockpit with Joker and Shepard.
"What the hell are we gonna do without that turian?" She asked.
Joker shrugged, "Throw a party? OW!"
He yelped as Cynthia kicked his chair.
"Brittle bones! Remember?"
"Oh I remembered. Let's go. Next stop is the Citadel?"
Shepard nodded.
Jacob had already said his goodbyes and left, so it was just Miranda standing in the Zakera Wards with Shepard. She was struggling to talk. "Shepard I just... No, I felt I... I'm sorry. I'm sorry for everything that happened with you and Cerberus."
He nodded and let a warm smile overcome him, "I know, Miranda. Take care of Oriana, okay?"
She sniffled, holding back tears, "Okay. I promise. And you know that when the Reapers come-"
"You'll be there. I know. Goodbye Miranda Lawson. And thank you-for everything." He embraced her for a few seconds and let go. Within a few more seconds, she had vanished into the crowds.
He walked back towards his ship, opening his comms to talk to EDI, "How much money do we have left?"
"After the amount we stole from the Illusive Man, our accumulated funds, and what we spent rebuilding the Normandy after the Collector Base, we have 2.5 billion credits."
"Begin depositing money into the accounts of Jacob Taylor and Miranda Lawson in small enough amounts that it'll go unnoticed. Hell, add to that list the crew of the Normandy SR-2 and their loved ones. And the crew of the SR-1, and the families of everyone who died on it. And the Richard L. Jenkins memorial fund-the Kaiden Alenko one too, and Torfan as well. Nihlus Kryik's memorial fund, the 'Rebuild Eden-Prime' charity. And make sure that you find a way to get all of our money into an account so that Alliance can't take it."
EDI's response to this long-winded request was a simple, "Yes, commander."
Shepard stood on the bridge of the Normandy with the remaining crew: Joker, EDI, Cynthia, and Chakwas.
"Are all prepared?"
They all nodded and affirmed that, yes they were.
He nodded. "I'm taking a shuttle from the hanger bay. That'll get me far enough away. I can't contact any of you while I'm on the run. When the Reapers arrive, people will get desperate and I can come back, but I'm not going to spend the last months of my life in a fucking holding cell."
He began to walk away, but turned back. "It's been an honor to serve with you. All of you." He saluted them. They-all except for EDI of course-saluted back as he walked to the elevator.
The moment his shuttle was free of the Normandy, the ship hit the mass-effect relay and headed to Earth. Shepard, on the other hand, began flying towards the planet before him.
He radioed down on a secure channel, "Wrex, it's me. Project Lazarus is dead. Initiate Operation Orpheus."
Orpheus is the guy who went to Hades and came back. Lazarus is the guy who returned from the dead. Neat, right?