For a moment, Shepard can't understand why she's surprised to wake up without pain. She's had painless awakenings before, obviously, and-
And then she remembers. Harbinger, the beam. The citadel, and Anderson and the Illusive man. The Catalyst and his three bad choices, and-
"Did it work?"
"Did what work, Commander?" Chakwas asks.
"The Crucible! Did it work?" Shepard tries to sit up, but Chakwas gently pushes her back against the pillows. "Where's Garrus? Did the Crucible fire? Is EDI okay? Are the Reapers-" she's babbling question after question, not taking the time to finish any of them or wait for answers, and Chakwas is…staring at her.
"Commander?"
Her head snaps to the left so quickly she hears her neck crackle, and her mouth shuts with a click.
"Kaidan? But you're dead!" Dead three years and she still sees him in her dreams, and that's the moment when she realizes that this is not the brightly lit, spacious medbay of the SR-2. "This is…this is the Normandy. The old Normandy."
She's right and she knows it – it even smells like her old ship, her first command, and she puts her head in her hands.
"Commander, how are you feeling?"
"This is all wrong," she says. "The SR-1 is gone. Blown to bits above Achera two years ago."
"The Normandy-" Kaidan tries, but she cuts him off.
"And you're dead. I killed you on Virmire three years ago, and we didn't even have your dog-tags to give your mother." She's not making any sense and she knows it, and she's saddened by the look of concern on Kaidan's face.
"Shepard?" and this voice gives her a flicker of hope and she looks up and grabs the sleeve of Anderson's uniform, desperate to make him understand.
"Admiral. Thank God. Eden Prime, it was Saren, sir-"
"I'm not an admiral, Shepard," Anderson says, but she hardly hears him.
"The Reapers are coming, sir, we have to….we have to warn the council, start preparing. Billlions died, billions died, I have to, Sir, you have to listen we have to stop them!"
She's still talking, still trying to make him see, when Chakwas sedates her.
Psychotic break due to unforeseen interaction with alien technology is what the psych evaluation says. For your own good is what they say as they lock her away.
She spends six months screaming the truth through the barriers of her cell, telling her story over and over to therapists and counsellors, and she knows they're not listening but she can't stop herself. She pleads for them to bring Garrus to her, just once, but they never do, and she spends the hours when she is too hoarse to talk anymore thinking about his face and his voice and his unshakeable trust. She probably doesn't want him to see her like this anyway.
They bring Kaidan instead, and he's sad and she knows he feels guilty. They think the beacon drove her mad, and he thinks it's all his fault. So he comes once a month and he sits with her for an hour and tells her about his life while she wishes he would go away, or die, or turn into Garrus.
She spends the next two months silent and unmoving, and they have to hook her up to IV drips to keep her fed and hydrated. She doesn't care. She doesn't have the strength anymore to fight, and she begins to wonder whether they may be right.
But no. There's no way she dreamed the last three years. No way she dreamed him. She keeps him as a talisman against her doubt, telling herself that he had faith in her and to do anything less is a betrayal of him.
She wonders if when she dies this time, she'll have another chance. As she lies on the bed unmoving, she thinks of all the things she would do differently as she does, and it slowly becomes a plan. The Plan, she calls it.
She doesn't record any of it. It's just in her head – just like you and Garrus and the Collectors and the Reapers, a traitorous little voice says in the back of her mind – but she goes through it again and again, refining and polishing it until it deserves the capital letters.
She's not surprised when Sovereign smashes through the Citadel's defences like so much tissue paper. They wouldn't listen, they weren't prepared. The Destiny is destroyed only a few moments in, with the whole Council on board. She's not sorry about that.
She's been waiting for so long, it's almost a relief when the geth smash down the door to her cell.
"What took you so long?" she asks.