I have killed everyone and am back in the cave as Desmond. It would appear that earlier in the game I was supposed to put the cube thingy in a control panel and that opened a door near the animus. I didn't do this at the time and am only doing it now right at the end of the game when, I presume, I am supposed to using the amulet to open the Door at the end.
I had a chat to Juno and now their doesn't seem to be anything to do. Dad and Lady just keep saying the same thing and the sarky bloke just tells me to get back in the Animus (which is clearly wrong). Anyone else come across this? Any ideas? I have looked on YouTube and it just shows them going from killing Charles Lee to getting back to Desmond and them all strolling off to the big door with the amulet.