Aeon tries to unlock doors on each floor but is killed by RU-486 who unlocks the right door but does not know that it was a plug inside that whould have kept the structure from sinking. This one was confusing. The origin of it all. Here it is shown as one 12 minute clip. Aeon is gunning down tons of Breen soldiers and periodically checks a map.
People also seem to be infected with a disease spread by a bug.
Trevor is involved with it and apparently has the vaccine and politcal power. Aeon comes across two men fighing over a brief case. She kills one and takes it. Inside is a jar of liquid wich she poors out without really knowing what it is. Aeon watches Trevor as he gives a woman the cure and also sees the news broadcast that warns of the virus.