5. The Silence, Seasons 5, 6 & 7
The Doctor enters into a stalemate on the planet Trenzalore, with the universe poised to start a second Time War should the Doctor speak his name. This causes a splinter group from the Church of the Silence (formerly known as the Papal Mainframe) to attempt to prevent this situation from arising by travelling back in time to kill the Doctor. First they blow up his TARDIS with River Song in it, but not him, causing cracks in reality that are causing the situation they are trying to prevent. Then they learn that Amy Pond is pregnant, kidnap her and steal her baby (who will turn out to be River Song), pretend to let the baby be returned to Amy so they can get away, then brainwash the baby into killing the Doctor (while dressed in a modified astronaut suit because this is what happened at a fixed point in time) only for the child to escape, befriend her parents when they were children, meet up with the Doctor again when theyre all adults and almost kill him but change her mind at the last minute. So then the Silence kidnap her as an adult and force her into a modified spacesuit to kill the Doctor, only for River Song to refuse which creates an alternate timeline where the Silence lay a trap by allowing themselves to be captured and confined in one place so they can kill everyone, but this plan fails as they all get killed and the timeline gets deleted because River changes her mind and goes back to the point where she does kill the Doctor except it isnt the Doctor its a shapeshifting robot full of tiny people, The Doctors survival means that, in his future, hes able to enter into a stalemate on the planet Trenzalore with the universe poises to start a second Time War should the Doctor speak his name. If anything this one makes more sense written down.