FireEye wrote...
I think I did neutral ("You don't sound happy to see me,") ... something, neutral ("the Alliance sent you in to investigate me, didn't they?"), something that didn't make sense, and neutral ("So long, Kaidan.") I also thought I still got the "Goodbye and be careful," but meh. I combed through it a bunch of times looking for a good permutation, and none of it really fit for me.
Personally, I think Shepard's a damn dirty traitor, but that's just me. 
Pfft, how do you think I feel?! My Shepard is a Sole Survivor, Kaidan should have knocked her on her ass for working for Cerberus. If Toombs shows up in ME3 my Shepard is going to take whatever punishment he gives her and be grateful for it.
Okay admit I might be lying about the "So long Kaidan" not getting the "Goodbye and be careful." I'm going by secondhand accounts. I'm to afraid to try, plus that fight is a pain in the ass, especially on the harder setting. (I guess if I was smart I would turn down the settings. But I would have to be smart to do that and god knows I ain't that) So exploring the different dialogue choices is a major pain in the ass.
Also I'm scaried to death that if Horzion isn't handed just right we might lose Kaidan. I hope Bioware doesn't get us with the little dialogue choices we did in ME2. Like not confirming your relationship with Kaidan to Kelly and such. On a side note, Kelly scaries the holy hell out of me. She is so harmless acting and from reading the books and just being all around paranoid, I hate admitting to her and risk Kaidan being use by Cerberus against Shepard. There would be a major reckoning if that happens, just sayin'.
@Chair Picture - not that I'm saying Kaidan should be covered. But wouldn't sleeping without a blanket be kind of cold?