My favorite headcanon is that Shepard doesn't have a very good time rejoining the Alliance after working with Cerberus - partly because he nuked the Collector base -removing much supporting evidence- and the Alliance is mostly certain he is an indoctrinated Cerberus husk.
Earlier, when it had become clear that Shepard had made Arch Angel his second in command, the illusive man decided to recover Miranda's usefulness by moving her off the SR2 and covertly inserting her into the Alliance as a foreign intelligence asset. This proves foresightful: after Shepard's return -in custody- Miranda is well placed to "handle" Shepard for the alliance.
The events of ME2 were not kind to Shepard. He lost colonies, he nearly got his entire crew killed, the love of his life turned away from him on Freedom's Progress - not even knowing if this was an act of walking away, or staying true to the "real" Shepard. Most importantly of all, Shepard once had a protege. A son. And then a brother - the one other commander John could turn to - who understood what it meant to lead men and to kill them because he had to. And Shepard got Arch Angel killed.
As Captain Miranda Lawson takes Commander John Shepard on the first few missions of ME3, they are tentatively feeling out a whole new relationship. She is trying to maneuver Commander Kaidan Alenko into Shepard's path - still playing TIM's game of blinding Shepard with close friends. But she is also coming to depend on him personally - to keep her secrets, to save her ship, to bring unity to her crew, to complete his missions, and in the end... to save her from enemies she has never been able to face. Her father. Kai Lang. TIM. And herself, her own genes, and her own fears, and the deep-seated belief that she should never have existed, and can never do good, no matter how much pain and suffering she tries to pay for it.
Shepard comes to trust her, to depend on her for the detail-mindedness and coll dispassion that must mean she will always be Captain. Thing start to get dicey though, as the worsening situation push everyone to their limits. Shepard is literally breaking, James is seemingly trying to find risks too big to escape, Edi is desperately searching for a way to define herself in the midst of Reaper lies and the unsolvable corruptibility of machine and flesh.
And then, all at once, Kaidan is on board the Normandy again. But Miranda is not with Cerberus anymore. Here is another Commander, a powerful intellect and a driver ideologue in his own right - and all the reasons she wanted him have become obsolete. Nor is his return absent fresh complications. Shepard clearly loves him, but Kaidan himself has not yet accepted him, and Miranda knows Shepard is poised on the blade of a knife between hope and despair. Then there is Jimmy - James Vega. The universe is a bleak place, right now. The Normandy SR2 keeps taking her crew to failed battles and hopeless people. Shepard is still reeling from losing Garrus, and he can't decide if he should allow himself to love ALenko or not. But Vega has no such complicated qualms. It's in his nature to compete - to be the best, to play the hardest, to risk everything. He doesn't think the Commander should risk romantic entanglements either. Nor does he think Alenko should have to deal with his pain all alone.
Joker plays off the ridiculously volatile chemistry, cracking jokes around every corridor. The truth is that he misses Garrus being there to sharpen his wit. He misses Kasumi's quietness - her ability to draw out from him the conversations no one else (not even Shepard) think he is capable of. He misses Wrex and Samar the most, perhaps, because they were the one who Shepard would let himself be open to. The ones he would let himself be less than, and Joker - for all his loyalty - doesn't believe any one man, all alone, can save the galaxy. But that's just who he is, isn't he? One man. All alone. He's fascinated by Edi. No one, not even she, believes so much in the rightness of all that she can become. He feels for her, he feels her potential like he felt his own. Just like he knew he could fly before he ever had engines, he knows she can know herself, and those around her, whatever she is lacking. But all too often, he feels her leaving him behind. It's easy for Edi to talk to Joker and Liara at the same time, but Joker can read the logs. Maybe what Edi can become is wonderful and right. And maybe he won't be able to understand her when she becomes it. It frustrates him. It hurts him. He is determined to love her so much that she never knows, never suspects, how much it does. And so he spends a lot of time talking to Dr Chakwas - at first. But though she knows a lot about treating illness, she doesn't know what it's like to be ... fragile. It's something Edi can never understand either. But there's someone who can. Someone who is deeply afraid of his affection for Edi, and who Joker must therefor convert. Someone who loves ships. Someone who's hurting.
Anderson is doing his best. Earth is fallen, but her soldiers still stand proud on her conquered lands. The SR2 is very nearly ready to return, and with her crew, do her last, desperate best as well. Shepard has passed a breaking point. He has felt sorrow and personal loss snap in his soul, and his steel is gone. He has been able to help so many others, but there is no one left to save him. He trusts and respects Miranda, and he will always follow her orders - hell, who was it that made him stop punching before he killed Vega, or Vega killed him? Who was it that talked Kaidan into speaking to him again? But she can't follow by his side. She's a damn fine captain, but she's not the warrior Garrus was. Or Kaidan is. Or Vega is. And Shepard can't go into battle and fail. He can't lose on Earth. And so he cannot choose to respect himself, to make only choices he admires, to preserve his dignity and his pride and the dreams he thought mattered so much. He has to live, he as to be able to fight. He has to be able to find a new peace, because he is not allowed to fail.
There is one last night before Earth. John knows the surprise on Kaidan's face will pass, that either he or Vega will beckon him, and that he will come - it was always that way. Maybe it's just what happens to biotics, or what their childhood (especially at Brain Camp) does to them. They are so terrified of power that they cannot let it go unwielded. They must touch it. They must own it. And there is no question any more, of who Shepard is, if he's still "him". Not right now. Shepard is wise enough to know there will be. That Kaidan will hurt, that the soldier will be forced to answer the question in the end. But tonight, all that there is, is three goddamn horny men and a tomorrow so bleak that any relief, any relent, must be accepted. Just that one time, Shepard was too slow. Vega is younger, after all. It shouldn't have surprised John that he reached out to Kaidan first. It hurts, and it stings, and it burns. But it also makes him feel alive, violent and passionate like never before. And so he makes it a part of himself.
The red tears through sky and earth, across building and horizon, through men and women. The red burns up, and it makes everything go cold. A beam, a terrible eye caught up in a whorl of black legs. The black legs! The red eyes! The Reapers! John runs. Vega runs. Alenko runs. Tali runs. Grunt runs. Liara runs. Running, running. Feet hit the ground, the ground hits back. The beams claw, bullets whine and men and women and husks shriek. Banshees scream. The beam, the beam. One red. One blue.
But Shepard told him how it had to be. In the darkness, when the man they both loved was sleeping. Shepard's hand had caught Vega's throat, and for longer and shorter than he could guess, controlled his breath, controlled his very blood. And he was whispered. Don't let Kaidan go. There is always a price, always one mission that no one sees coming. But this mission is not for Kaidan, or for you. It is for me. Take care of him.
Shepard's mind has never been so clear, his pulse has never before raced through every fiber of his being, his sinews have never stretched to far and snapped back to fast and refused so perfectly to creak and strain. He is not plowing through the pain of combat - his every cell has awakened, and there is no pain. He is focused, he is a laser. And maybe that is why Harbinger sensed him, like a spark at the edge of sight. A bright thing. A living thing. A enemy utterly inconsequential, and yet to dangerous to allow.
Even then, John Shepard would not have fallen. Even Harbinger's eye could not have caught him - not then. But Vega caught him. And suddenly Shepard's world turns red red red. The red is everywhere. There is only cold. Kaidan hears him. For one singing moment, he almost stops. And Vega almost won. Almost got to spend his life instead of the others'. But Kaidan loves him. In that moment, when his eyes refuse to see Vega, to even consider coming to his aid, he knows he loves Shepard. And because he loves Shepard he does not stop. Vega pushed Shepard into the beam, gave himself the time to take his place and save the man Kaidan loved. But he also gave Kaidan a moment to do the one thing he never counted on.
And then he is falling. The blue armor. The beam is all white now. Darkness is closing down. Harbinger is flying away. There is a shuttle. The sound of a shuttle.
For a long time, the blackness is cruel and wicked. The shaking and the heat crawl into every bones, smashing the teeth that nature so carefully planned, ripping apart eardrums - did you know, nature is so cunning, they can sense vibrations as small as a hydrogen atom - undressing bodies and undressing brains. But then the shaking stops.
The blackness becomes gray. Arms. Warm. This is the rough skin of a warrior. "Kaidan?" But there is not answer. Not in words. Only the sound of a man weeping.
...To be continued.