This is basically the result of my first playthrough of the Suicide Mission in ME2. I lost people because I had no idea of what I was doing and didn't have any DLC yet. I felt like shit about it.
It's been six months since Earth Systems Alliance hauled Shepard in for questioning on her mysterious resurrection and affiliation with Cerberus. Six months wasted on answering the same questions over and over. Yes, she did indeed perish with the first Normandy over Alchera, or so she believed. No, she was not in league with terrorists before the Collectors' attack. Yes, she did feel it prudent to join forces with them, because you were clearly not doing your fucking job, Admiral Lee.
That last remark earned Shepard a period of peace in the very comfortable room in an Alliance owned apartment building. In fact, it seemed as they had left her alone altogether. It was obvious that the heads of the Alliance did not know what to do with her, probably wishing she had never made it back from what lay beyond the Omega Relay.
Six months ago the news channels across the Milky Way blew up with images of Normandy SR2 being escorted through the Charon Relay and the apparent arrest of the rogue Spectre, who escaped death twice, stopped attacks on human colonies and caused the destruction of one of the largets Batarian systems. The Citadel Council once again found themselves in a very sticky situation. They were dealing either with a mad woman or a prophet. The evidence Shepard brought back with her were far more tangible that two years ago, yet there was still a possibility that it was all a ruse by Cerberus who may or may not be using the Savior of the Citadel to cause panic and destabilise the political balance of the galaxy. So they took the easy way and left it to the Alliance to deal with its own.
At first Shepard was relieved to be back and not handed over to the Batarians. As time went on, she grew frustrated and resentful. Harbinger's last words were fresh in her mind, she had only postponed his arrival. Now she regretted deeply turning herself in instead of trying to find support elsewhere. Or she did when she could bear thinking about her situation at all. The last few days of respite meant that she didn't have to deal with the inane questions that would never help solve the oncoming problem. It also meant she was left to her thoughts, that were now focused on the bleak future and the consequences of her choices.
She did not feel remorse about Bahak. Try as she might, she couldn't think of any other way to resolve the situation and felt it was useless to dwell on. She had no choice then. But she could not stop dwelling on the time when she did. That desperate charge through the Omega Relay and what followed. Every time she closed her eyes she saw not the supernova at Bahak, or the giant human Reaper, or the first Normandy burning in Alchera's orbit, but the three coffins.
Jacob...
She could tell herself that he volunteered, that he was fully aware of the risks. But the truth was that she could not bring herself to risk Tali's life. Not because she was an Admiral's daughter and an excellent way to garner support from one of the largest fleets in the galaxy. When the choice landed heavily in her lap, the brave Commander chose Jacob, because he was Cerberus and Tali was her friend. Jacob, who was there from when she woke up and was every bit Alliance she was before her first death. Jacob, who died because she made a selfish choice.
Thane...
He was a trained killer. He survived many battles and had gotten himself out some very tight spots. Shepard trusted his quick thinking. Besides, who else could she have chosen? She needed Garrus by her side and no one else had the battle experience. He would be careful and if needed to, shield his team from harm. And he did in the end. Thane, a dying assassin who only just started to reconnect with his son.
Miranda...
In some ways, it hurt more than leaving Ash on Virmire. Ash was an impossible choice, Alenko was a far more valuable soldier and he was guarding the bomb. Miranda was a mistake, the biggest Shepard ever made.
Things were not fine between them when Shepard ordered the Normandy through the Omega Relay. They had just come out of an explosive fight with Jack who put Shepard on the spot. But this time around Shepard's diplomatic skills failed her. Angry with Cerberus dealings on Pragia, she sided with Jack in hope of defusing the situation at a more convenient moment. But the moment never came. She tried talking to Miranda before going off to examine a dead Reaper, but was greeted with short dismissal through gritted teeth. And then the Normandy was attacked and they had to go after their crew. There was simply no time to tell Miranda that she understood and that she was grateful for everything. So she kept Miranda by her side, not because she didn't trust her, but to keep her safe and together with Garrus they tore through waves of Collectors to the center of their base and the horror that lay there. When it was dead and the Illusive Man was pleading with Shepard to turn the thing over to Cerberus, Miranda proved that the trust was not misplaced. She turned her back on the man she trusted most for Shepard.
In her deepest, darkest moments, Shepard knew that it was her fault. Miranda could have gone into the final battle with a clear head instead of worrying of following a Commander who questioned her value and loyalties. She might have had the time to throw up a barrier when they were buried by debris from the collapsing base. When she closed her eyes, Shepard saw the three coffins and the life flickering out of the eyes of the Cerberus operative. Miranda, who gave her life and a second chance. Who died because Shepard did not take the time to sort things out.
So yeah. Thank you for taking your time for my guilt trip. R&R, if you wish, as harshly as you please.