This episode also sees the return of this series' main villains, the Silence. As mentioned earlier, we don't find out why they blew up the TARDIS at the end of Series Fnarg, but we do get an explanation for their overall motives, although I do think that three seasons is a bit too far to stretch arc-based plots and plot points in general, especially if we have to wait a long time for the next season. I did feel they were used well here though and were genuinely creepy and properly alien.
Then there is the nature of the oldest question in the universe, the question that the Silence don't want answered. This question turns out to be "Doctor Who?" Not gonna lie, that was A) predictable and B) a bit of a letdown. It also doesn't really explain why the Doctor started fleeing when he heard it initially; from his reaction to what the disembodied head of Dorium Maldovar, the now headless man last seen in "A Good Man Goes To War" (and, in what has to be the stupidest line I've ever heard, the skulls in Maldovar's tomb are moving because they were "beheaded while alive"; generally when that happens the subject goes from "alive" to "dead") told him of the question.
The highlight of the episode was not Matt Smith's hilarious facial expression when the astronaut doesn't shoot him, or the fact that this entire episode came about as a result of the companions screwing up his plan. No, the highlight was the character Brigadier Alastair Lethbridge-Stewart (played by the late Nicholas Courtney, who passed away earlier this year) being given a send-off in-universe that tied into the plot and worked wonderfully as both an emotional scene and a tribute to one of the constants of Classic Doctor Who. If I was a more cynical man, I would suspect that the writers planned it that way.
After all that, the universe was saved from collapse by the Doctor returning to his original timeline where he had to fake his own death and the season ends on a happy note as it's revealed to the companions that he's alive but now travelling by himself. This fact was also revealed to Dorium Maldovar, who takes to yelling the "oldest question in the universe" at the Doctor as he leaves.