synopsis from http://en.wikipedia.org/wiki/The_Name_of_the_Doctor
In the beginning of the episode, Clara is seen falling through time and space, and appearing near several of the past Doctors. She claims that she has been running throughout history in order to save him, and that he rarely hears her.
Madame Vastra and Jenny learn of a prophecy told by an insane man regarding the Doctor; in particular, he claims to have a “secret” about the Doctor. They hold a “conference call” to bring themselves, Strax, and Clara Oswald across time and space into a dream realm using soporific drugs, where they explain the prophecy relating to the planet Trenzalore (“The Wedding of River Song”). The consciousness of the deceased River Song, saved in the Great Library in “Forest of the Dead”, also joins them. While in the call, Vastra, Jenny, and Strax are attacked by Whisper Men, strange faceless creatures. Thinking quickly, River forces Strax, Vastra and Clara to wake up. Clara wakes up back in contemporary London to find the Doctor looking for her.
Clara quickly explains what she remembered to the Doctor, including the apparent deaths of his friends. The Doctor decides that they must go to Trenzalore to save them. As he fires up the TARDIS, the Doctor explains that the prophecy relates to his death, and Trenzalore will be the place he is buried, and is the one place he should not go. The Doctor plugs Clara into the TARDIS’ port, allowing it to access her memory of the coordinates. The TARDIS resists, unwilling to cross the Doctor’s timeline, but he manages to crash the ship onto the planet, ravaged by a giant war in the past and covered in gravestones. One of the stones looks like an enormous, monolithic effigy of the TARDIS. The Doctor points out that the structure is not a tombstone, rather it actually is the future TARDIS, dying and thus unable to control its transdimensional functions.
The Whisper Men appear to attack the duo. Clara notices the gravestone of River Song, something the Doctor calls “impossible”, due to her physical death at the Great Library. River appears to Clara, and tells her that although she can see her due to the conference link, the Doctor cannot. With River’s help, Clara suggests that the gravestone is actually a secret entrance. The Doctor accidentally reveals River to be his wife, and he and Clara crash through the stone. Elsewhere, Vastra and Strax find themselves outside the giant TARDIS, along with Jenny’s comatose body; Strax manages to revive Jenny before they are surrounded by Whisper Men. The Whisper Men are part of the Great Intelligence and are led by Dr. Simeon (“The Snowmen”); although he has died, he remains as a conduit for the Whisper Men, who can shift their appearance to look like him. While Clara and the Doctor are running through the telepathic fields of the dying TARDIS, Clara begins to remember the events of “Journey to the Centre of the TARDIS” through the telepathic link with the TARDIS. The duo soon arrive outside the giant TARDIS, where they are held along with his allies by Simeon and the Whisper Men.
Simeon demands the Doctor say his true name or else he would have the Whisper Men stop his friends’ hearts. The Doctor refuses but River Song appears at the last moment, having said his name and allowing the doors to open. Inside, a pulsating column of light sits where the console would normally be. The Doctor tells them that it is the scars of time travel that he has left on the universe. Simeon declares his intention to climb inside and undo the deeds of the Doctor’s past; though Simeon knows he will die, the act would destroy the Doctor. His entrance into the column sends the Doctor to collapse on the floor, as he is “dying all at once.” As the Great Intelligence disappears, Vastra, Jenny and Strax find that stars outside are going out, erased from existence by the new timeline. Jenny also disappears, and Strax denounces Vastra as “reptile scum,” forgetting that they are friends. Vastra is forced to kill him to save herself, and she runs back inside.
Clara’s knowledge about her existence deepens, and she realizes that if she also enters the timeline, she will be able to save the Doctor from Simeon’s meddling. River appears and tells her that she will not be able to come back, and the Doctor tells her not to go, but she decides to enter the timeline anyway. She calls to the Doctor, “Run, you clever boy. And remember me.” before she enters. The events from the episode cold opening play out, where she witnesses events from all of the previous incarnations of the Doctor and helping him along (including from “Asylum of the Daleks” and “The Snowmen”). Having saved the Doctor’s timeline (subsequently restoring Jenny and Strax along with the rest of the universe), she finds herself falling indefinitely and considers her role as the “impossible girl” done.
The Doctor is able to wake up, and he decides to rescue Clara by entering the column of light. River, who believes he cannot hear her, yells at him to not be so stupid and tries to slap him; however, he is able to catch her wrist. She sadly asks why he has been ignoring her, and he tells her that he does not know how to say goodbye to her. River says that she will only accept a goodbye spoken as if they will see each other again; the Doctor does this, and River fades away. The Doctor jumps into the timeline in an attempt to save Clara.
[i]Clara falls into a cavernous place, and sees ghosts of the past Doctors race past her. The Doctor’s voice guides her to catch the leaf that was responsible for her life (“The Rings of Akhaten”) and helps her to find him as the space around them collapses. As they are about to leave, they spot one more figure nearby, whom Clara has never seen before. The Doctor reveals this is an incarnation that didn’t even hold the moniker of “the Doctor” due to his actions in life. He explains to Clara that his real name is not the point; he chose the name “the Doctor” and the name a person chooses is like a promise, and this unknown incarnation is “the one who broke the promise. He is my secret.” This unknown incarnation responds by defending his actions, stating he had “no choice” and that he did what he did “in the name of peace and sanity,” which the Eleventh acknowledges to be true but not “in the name of the Doctor.” The figure (John Hurt) turns to look at them, as the screen credits identify him as “The Doctor”.
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