The Eleventh Doctor

 Current Doctor, played by Matt Smith

First full appearance: The Eleventh Hour

The Eleventh Hour

 Having regenerated for the 10th time, the newly incarnated Doctor, crashes a damaged TARDIS into the garden of  seven year old Amelia Pond. The year is 1996.
Amelia tells the Doctor of a large crack in her bedroom wall, which the Time Lord examines only to realise that it is a crack through time and space itself.
Opening up the crack briefly, reveals an Atraxi prison and soon after, the Doctor receives a psychic message relaying that "Prisoner Zero has escaped".

 When the cloister bell from the TARDIS rings, the Doctor goes back to the time machine in order to fix it, telling Amelia that he will be back in five minutes.
Amelia packs her bags, ready to travel with the Doctor and waits patiently in the garden for his return.

Amy and Prisoner Zero

 The Doctor meanwhile, having thought that he had only been away for 5 minutes, actually returns 12 years later. As he searches the house for Amelia, he is knocked unconscious and handcuffed to a radiator. When he awakens, he finds that his assailant is a now grown Amy Pond, who doesn't recognize him.
Unwilling to believe who he is, having spent the last few years being being ridiculed by the village for her tales of the Raggedy Doctor, it becomes obvious that there is something in the house.
Retreiving the Doctor's Sonic Screwdriver, which had fallen when he was attacked by Amy, they escape and flee the house.

The Atraxi

 Very soon the Atraxi arrives and threatned that if Prisoner Zero is not returned, then Earth will be destroyed. The Doctor now has a few hours, to find the Prisoner. This does not prove easy as the Prisoner is a 'Multiform', able to take the form of those who are unconcious, his first victims being the coma patients at a hospital where Amy's boyfriend Rory works as a nurse.

Borrowing a laptop and interrupting an online meeting of several scientific experts, the Doctor relays some instructions to them before rushing to the hospital and rescuing Amy and Rory from Prisoner Zero.
The Doctor outlines his plan, which is that he has created a virus that will broadcast the the number zero, around the globe. This is connected with Rory's phone which contaims images of the coma patients that he had previously taken.
However Prisoner Zero knocks out Amy and  having been in her childhood home whilst she was growing up, creating a kind of bond, adopts the form of the much younger Amelia as well as the Doctor.

The Doctor giving the Atraxi a good telling off.

 The real Doctor manipulates her subconcious into remembering what she had seen in the house which reveals Prisoner Zero's true identity. Having now been located by the Atraxi, they take him away (after he tells the Doctor that "silence will fall") but not before the Doctors calls them back and tells them that others have also invaded and threatened Earth and have not been successful, making it sound as though they had been defeated by him.

With the Atraxi gone, the Doctor goes back to the TARDIS and leaves before Rory and Amy have had a chance to say goodbye. On his return to Amy's house, he finds that another two years has passed.
Still angry with him, Amy decides to travel with the Doctor but only if he returns her the next day. The Doctor agrees saying that he chose her because he is lonely but really it's because he wants to keep an eye on the crack that still appears in Amy's bedroom wall.