Last night I was playing the game on sequence 9: "the foam and flames", I was in the part in the brewery and then guys lit it on fire. I was playing the game at like 3:00 am so i thought this was a good time to quit, since it had autosaved.
The next morning, which was today, I start up the game and see that i've spawned near the borders of New York, and not only that, the mission marker for the mission had disappeared completely. So, I've spent 3 hours or so trying to find ways to play the mission again. I did all the side missions in New York, that didn't work, went to the frontier and came back, that didn't work, even exited out of the Animus, and while I did see a few new cutscenes and unlocked a few new rooms in this ancient place hidden in a cave, when I went back to the part of the game with Conner, the mission still hadn't appeared again.
So, here I am, I ask you fine people of these forums to help me out, because I seriously cannot find a way to do this mission so I can proceed in this game's great story. :(