The more I think about it, the more I love Days Four and Five. Because, like with Angel on AtS, Jack was why I tuned into the show in the first place, and watching him just give up is a wonder.
Maybe it cheapens Ianto's death - no, I know it does - but that's what Ianto was there for. That's why Alice and Stephen were there, too.
Ianto was doomed from quite early on in s3 (well, originally he was doomed in s1 and s2, as well, but the writers went around and changed it both times), but there were all those red flags I kept ignoring, because he was my darling character.
If Inato had lived into Day Five, Jack wouldn't have made the choice to use Stephen. He wouldn't have made it that easily, at least. Because standing by his side gets you killed, and he finally learned this, and like
meret said, he's only using his head from that point on, because using your heart is too painful.
So he gives up and runs away. He's a god with nothing left to lose, because he's already lost everything. He's died and died and died, and it never works out well for anyone he cares about.
Also: whatever happened to Susan? Did the Doctor get her killed? Are we that far into the parallel by now?
Also two: Man. I want SO MUCH FIC I can't even begin to tell you guys.
Alice/Johnson, Jack/John, Jack/Doctor, plain Alice fic, and Gwen fic, too. And some Awesome All Lady Torchwood! And fixits, too, because sometimes I do like my happy endings.
ETA: It just struck that when Jack's sitting in the hallway waiting and Alice comes in through the door, the shot and the posture are exactly like Jack - a million lifetimes ago - in the Gamestation prison, straight-back, just waiting for the Doctor's orders. Alice leaves and he deflates, and then he's off into the sunset. That moment is when Captain Jack Harkness dies. Whatever he is after, it's not Captain Jack anymore.