A Biography of the Doctor
The Eleventh Doctor
The Doctor has fallen out of the TARDIS, and manages to climb back in as it flies over London. He gets back in, and the TARDIS dematerialises. When it rematerialises in a small English village, he has to use a grappling hook to climb out of the swimming pool, which is in the library. He meets a young girl called Amelia Pond, discovers that a crack in her wall is actually a crack in space-time. He closes the crack, but discovers that prisoner zero has escaped through it. Before he can investigate, he hears the cloister bells, and knows that the TARDIS engines are phasing - he has to dematerialise the TARDIS to fix it, and promises Amelia that he will be back in five minutes. However, he actually comes back twelve years later. Running into the house, he is knocked out by a cricket bat.
He wakes up, handcuffed to a radiator, with somebody dressed as a policewoman standing over him. She says that she lives there, and he points out that there's a door on this floor of the house that she's never noticed. She goes in, finds the Doctor's sonic screwdriver, and prisoner zero, before running out. She hands the Doctor his sonic screwdriver, and he uses it to lock the door. However, prisoner zero breaks it down, disguised as a man and his dog. The Doctor and the woman, actually Amelia (now calling herself Amy), escape the house.
The Atraxi, who are the prison guards, send a message to the world that "Prisoner Zero will vacate the human residence or the human residence will be incinerated", and the Doctor figures out that they're talking about the Earth. And they have surrounded the upper atmosphere with a force field. He locates prisoner zero, who has left the house, as a nurse (Amy's boyfriend Rory) is photographing a coma patient wandering around the village - the same form of a man and his dog, which Prisoner Zero is imitating. He attempts to use his sonic screwdriver to alert the Atraxi, as they're scanning for non-terrestrial technology. Unfortunately, it overloads, and prisoner zero escapes down a drain.
The Doctor sends Amy and Rory to evacuate the coma ward of the hospital, and borrows a laptop from another of Amy's friends. He gets himself in on a conference call between NASA, Jodrell Bank, Tokyo Space Centre, the European Space Agency, the (Australian) Commonwealth Scientific Industrial Research organization, and Patrick Moore. He gets them to distribute a computer virus that he writes on Rory's phone, which sets all counters that catch it to zero. He then joins Amy and Rory at the hospital, confronts Prisoner Zero, and leads the Atraxi to him.
As the Atraxi leave, he calls them back, citing Article 57 of the Shadow Proclamation that their actions are illegal. He confronts them and points out that the Earth is defended, sending them away permanently. He returns to the TARDIS, which has redecorated itself, gives her a quick hop to the moon and back to run her in, and returns for Amy, arriving two years later. She agrees to travel with him, despite the next day being her wedding day.
(This follows on from the Doctor's regeneration in The End of Time)