As confusing as an episode of Lost, as baffling as an episode of Twin Peaks, and I'm as nonplussed as at the ending of The Prisoner or of Quantum Leap. This season is not a young children's show. It does look good visually though. I hope I do understand it before the end.
Ah! So, it's my childlike mind that's kept me from fully understanding what's going on. Either that, or the creative minds here have had way too much time to brainstorm between seasons. (What's it up to, now, five years?

)
Anyway, I've watched this episode twice and consulted Den of Geek wisdom, so I think I've got a better grip on what's happening. Maybe.
I thought that the Time Lords and Gallifrey were the ultimate time authority, with the Doctor as the loose cannon who regularly saves the Universe. All this while, it's been the Mouri and the planet Time keeping time from running amok?
Also new, at least in my finite memory, is the concept of an immortal battle between time and space.
The Flux has wrecked space, thereby permanently disturbing time. The Doctor is somehow responsible for the Flux, according to the authoritative older woman who confronts her near the end of the episode and pronounces the Universe dead.
Who is she? Another previous or future Doctor?
With Sontarans, Cybermen, Daleks and Weeping Angels all taking advantage of the chaos, it seems unlikely that the Doctor will be able to once again save the day. I have a feeling that the Weeping Angel's hijacking of the TARDIS will be key to the solution. After all, their specialty is pushing people back through time.