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Have you made sure you have pressed all the green buttons, I was a bit of dumbass with this. I scaled up the scaffolding and such, and pressed all the buttons (bar the ones on the ground floor). I think I over complicate thinks.
If that doesn't work, try heading back up to the animus to see if there are people there- there should be. If not, then sorry I can't think of anything else.
You are not supposed to exit the Animus between Sequences 11 and 14. I was reading here about some people that powered down during the cutscene, effectively sealing themselves somewhere they weren't supposed to enter in the first place.
As far as I know from that topic, you're screwed. Sorry bud.
"If I am what I have and what I have is lost, then who am I?
Thanks for all the advice. Desmond is the only one around. I guess the game wasn't finished saving when I quite. Others are having the same problem. Too bad this game saves over all previous saves. Guess I'll delete and start again.