Okay, so... I think we've seen the last of The Silence. I realise this is probably obvious, but;
- A prophecy is made about Trenzalore, and the events that occur there. The ramifications are severe, we're aware of that. The timeline of The Doctor is tampered with, which has horrific implications for the universe he's done so much to develop.
- A religious order intent on bringing about a "Silence" to the Great Intelligence's answered question is created; i.e. "The Silence" that "MUST" fall. They first attempt to either kill or ground The Doctor by destroying his TARDIS.
- Separately, a well meaning but ultimately ill-informed group of The Doctor's most prominent adversaries devise the Pandorica, and seal him within this prison, presumably to simply stop him from doing anything rather than killing him outright.
- We see that The Silence aren't that clever... they're trying to stop the effects of Trenzalore, but by doing something like blowing up the Tardis they're fucking up the universe just as badly.
- Universe gets remade. Silence still exist. Silence & The Silents (alien) are seperate. The elaborate plan to murder The Doctor at the fixed date of his death (was this always known? Timey wimey!) is concocted. You can argue they're doing this for the good of the universe, but the plan to have him killed by the child of his friend is just them being arseholes.
- The Doctor "dies", to all intents and purposes. The Silence are watching at Lake Silencio and see this is done. The Silence disbanded?
- Trenzalore happens anyway. The Silence that "must" fall does not. The Silence are fucking idiots. The Doctor defeats them, but it's a bittersweet victory because now ValeHurt has been unleashed.