What Happened at the End of Resident Evil: Revelations?

Resident Evil: Revelations has one of the most complex and tangled narratives that we've ever seen from the series. The amount of inner organizational drama, new characters, multiple sub-plots, topped off with the fact that Clive was playing games with us the whole time can make for some very confusing moments as you try to recall where certain events occur within the timeline. So today we're going to be taking a look at this game and explaining some things I think can be confusing about the story as well as the ending cut-scene which plays into RE5... sort of. But, to begin let's hit a brief overview of the story to get you in the mood.
What Happened at the End of Resident Evil: Revelations?