as far as i can tell, Thanatos, James, and Byrne are a nanosecond behind in time somehow, so no one else can see them. they're trying to find Marshall Sanchez, the last person that happened to. your two characters and Felix and Deomi are doing...i.whatever it is you're doing. Nami is taking the girl he rescued from the devil-baby-thing with him, while we dramatically see it isn't dead. Varlow is being lead to Nami by Alex, talking to him in his head, who is in another world altogether. The angel/demon war is still going on as far as we know, after the
angels sundered the control of the Foundation, releasing most if not ALL of the highly dangerous SCPs from containment, probably causing the end of civilization and the world as we know it.
so yeah, thats a pretty condensed version of it.