A/N: I'm slow, what can I say? This chapter completes the story. This is sort of my own personal canon. You might not like it, and that's okay.
Shepard limps down the rightmost path, toward the tube. Somehow, the cylinder reminds him of the proto-Reaper on the Collector base. Why does it make him think of a Reaper? His choice is firmly locked in his mind. He's worked it out; the fog has lifted. He raises his hand-cannon and fires, his steps quickening, gaining in confidence, determination etched onto his face. He fires again and again and again, until there's a flash and the world goes red.
Little Johnny Shepard is watching cartoons with his father when they get the knock at the door. His dad puts down his beer and goes to answer it. There are two somber-looking military men standing on the stoop. He takes one look at them and turns to Johnny, his face ashen. Go up to your room, Boy. Johnny starts to cry. Where's Mommy? he wails.
Shepard is eighteen. His past misdeeds have caught up with him. The cops picked him up, arrested him for murder. There are witnesses. His lawyer tells him he's fucked if it goes to trial. He might be able to deal it down to manslaughter, but either way Shepard's looking at hard time. He says there might be a way out, if Shepard will meet with someone.
He's put in a room with some buzz-cut wearing an Alliance military uniform. The man asks him to demonstrate his biotics. He's skeptical, bored. Move a pencil or something, he says. His eyes widen when Shepard sends his briefcase flying into a wall. He retrieves the briefcase, pulls out some papers and a pen, slides them across the table to Shepard.
Shepard returns from Torfan. Most of his squad died. It was worth it. They killed every last damn batarian in that shithole.
Commander Anderson calls him into his office. That was a real clusterfuck, Son, he says. You got the job done, but you broke a lot of regulations. They're calling you 'the Butcher'. I hate that shit, but there's nothing I can do about it. Half of the brass wants you out on your ass. The other half wants to promote you.
Shepard remains standing at attention. Which half are you, Sir?
Neither. I'm putting you up for the N program. Congratulations. Now get the hell out of my office.
Miranda packs her bags. Shepard pleads with her not to go.
Her voice is thick with emotion. I can't do this anymore, John. You'd rather open up to that… that thing, than have one honest conversation with me. You won't let me in, but you'd let that monster swallow you whole? Fine. You want to destroy yourself, I can't stop you. But I don't have to watch it.
He pushes her against the wall. You want honesty? You need me. You burned your bridges with Cerberus.
She shoves him away, icy blue anger in her eyes. Thanks for making this easy, she says coolly. She takes her bags and walks out.
Shepard holds his hand out to the boy in the air duct. It isn't safe. The city is crawling with those Reaper things.
You can't help me, the boy says. A Reaper horn blasts the air nearby. It's hard to imagine a more dreadful sound. Shepard glances behind him as one of the monstrous machine-things strides past the shattered wall. When he looks back, the boy is gone, vanished into the ductwork.
Anderson calls to him. He leaves. The boy's on his own.
When he reaches the ocean floor, the Leviathan reveals itself. It boasts of being something more than a Reaper, something much older. It intrudes into Shepard's mind. What's real is no longer real. He finds himself on his knees, at its mercy, seeing the faces of people from his memories.
The Leviathans created the Intelligence, which in turn created the Reapers as a 'solution'. The Reapers have perfected indoctrination. They perceive Shepard as a threat. The Leviathans acknowledge that he is an 'anomaly'. In the end, they agree to help him.
He's an anomaly? The Reapers perceive him as a threat? They haven't seen the half of it yet.
Miranda asks him for access to Alliance resources. She can't say why, and he doesn't question it. He takes her hand before she turns to go.
I'm sorry, Miranda. The truth is that after you brought me back, I didn't feel… real. I felt like a golem, like something that didn't belong in this world any longer. I was filled with anger over having to return to all this pain. There's so much of it. It never ends. I shut you out because I knew you deserved better than to hear that from me.
She squeezes his hand. Shepard… she whispers, looking up at him.
He continues. I was wrong before. You don't need me. You never did. I'm the one who needs you, Miranda. Please…
Her lips crush against his, silencing him. They press their bodies against one another, desperate and yearning. When their mouths separate, she smiles at him and he knows all is forgiven. He lifts her and carries her to the bed. Everything will be okay, he tells himself. Everything will be okay.
Shepard opens his eyes. Miranda is with him, sitting on the floor, holding his head in her lap. Her face is covered in soot and grime, her lustrous hair singed, bodysuit ripped and charred all over. She's burnt, bruised, scraped, scratched, but she's okay. And she's here. She found him. Somehow she found him. She looks down at him, her brilliant smile a reminder of her near-perfection, however much the apocalypse might try to mar it. "Lying down on the job again, I see?"
He laughs, but his laughter quickly turns to coughing. She strokes his hair until he brings it under control. He looks to one side. The Illusive Man lies dead, a portion of his head missing. He looks behind him. "Anderson!" He looks back up at Miranda. "There may still be time."
She shakes her head sadly. "I tried, John. He's gone."
He sits up, suddenly. "The Reapers! I have to…"
She grips his shoulder firmly and points past the control panel, to the viewport. "Look. It's all over. You did it."
He looks out the viewport. It's true. The last of the Reapers are being systematically cut apart and blown to smithereens. They aren't fighting back. He looks to her. "We're winning?"
She nods. "Reports are coming in from all over. Their shields went down and they simply… stopped."
He furrows his brow. "But how?"
She laughs. It's a surprisingly free, unburdened sound, a sound he's never heard before. "I was going to ask you that. I found you here, taking a nap. What happened?"
He brings a hand to his temple. "I don't know. I thought it was a dream…" Was it a dream? A hallucination? Is he dreaming now? No. He focuses on the feel of Miranda's touch. This is real.
Miranda peers at him. "Shepard?"
"It must… It must have been some kind of mental interface. That's how the Crucible works. But that boy…the Reapers…they knew about it. They tried to interfere. To confuse me."
"Thank goodness it didn't work."
Something suddenly occurs to him. "The geth! EDI!"
Miranda looks confused. "What about them?"
"Are they okay?" He reaches to activate his comm. It's fried. "Can you contact the Normandy?"
"I think so," she nods. "Assuming EDI is still monitoring the old frequency." She adjusts her comm and puts it on speaker. "Normandy vessel. This is Miranda Lawson. I have located Commander Shepard. He is alive and well."
There's a few seconds of static, and Shepard's heart sinks. Then EDI speaks. "Miss Lawson, I'm pleased to hear that you and the commander are okay. We have your location and will rendezvous at the nearest suitable docking station shortly, pending authorization from Lieutenant Commander Williams."
"EDI," Shepard speaks. "Give me a status report on the geth forces."
"Data is still incoming, Commander. But it appears they have suffered minor to moderate losses. Most units remain operational. Their assistance was invaluable."
"Thank you, EDI. And EDI…"
"I'm glad you're okay."
"As am I, Commander. Now that you have vanquished the Reapers, I can enact my own plans to dominate the organics."
Shepard waits a beat. Then another. Nothing. "EDI?"
"That was a joke."
"See you soon, EDI."
Miranda kills the call and looks at him with a curious expression. "What was all that about?"
Shepard shakes his head. "Nothing." He stares out the viewport, wonderment on his face. He can see the Earth in the background. It's so… perfect. Miranda puts her head on his shoulder. He wraps an arm around her. Everything will be okay, he tells himself. Everything will be okay.