I thought this would be fun, to run through possibilities of what happens next. (Well, my brain's going this way a lot, so why not? LOL.)
Booth: in the immediate weeks, he'll be at the FBI, doing the kinds of things they've not shown us much of over the years - supervisory stuff, or case work that didn't need the kind of forensics that they did together;
Brennan: writing her next novel/possibly weighing in on what's going on at the lab during rebuild; maybe doing some consulting work at one of the other forensic labs in the area (which are suddenly having more to do, what with the Jeffersonian being down; I can see her winding up helping Booth with any non-forensic-focus cases he's got, too, because she's learned a lot about investigation in general
Cam and Arastoo: being parents; looking ahead six months, I can sort of imagine her coming back to the lab as chief pathologist, but maybe choosing to leave Hodgins in charge of the boss-headaches; Arastoo? Perhaps teaching? (How many forensic anthropologists can DC support?)
I wonder...with the Jeffersonian being blown up and rebuilt, if they could wind up with more funding, and more work (increase in tricky forensic cases from across the US)...enough for two permanent full time forensic anthropologists at the lab?
In the meantime...what do they do for a pathologist while Cam is out?
Angela: pregnant, they have a boy; to the best of my reckoning, he'd be about 2 1/2 years younger than Hank? (Based on how old Hank looks in The Day in the Life rather than any correlation with seasons; the show lives in BST (Bones Standard Time)
Wendell: I think it would be fun for Wendell to realize his passion is medical school so he can be an oncologist. It means more school, but I'm thinking for someone with his education and experience, he'd do fine with it.
Also: this one probably won't be popular, but hmm...catching some Wendell/Daisy vibes in the last two eps. That might be interesting.
Aubrey: this was my one nitpick about the episode, so one of the things that happens is he and Jessica work their way back to friendship. (And, in my head, eventually something more. I know that's not what MP said, but hey, there's an open field in front of us now and while Karen didn't annoy me as much this episode as the last few times we saw her, I still don't like her. Plus? It's too early for him for anything serious, so if they have a fling, it's a rebound.)