Flashbacks of the Doctor’s many lives reveal that Clara, aka the Impossible Girl, was born to save the Time Lord, but she doesn’t know why.
In London 1893, Madame Vastra receives news from a serial killer in prison that the Doctor’s greatest secret – one that he will take to his grave – has been discovered. She then summons his closest allies – Jenny, Strax, Clara and Professor River Song – in a time crossing ‘conference call’ to discuss what to do next. When River learns that the prisoner mentioned the word ‘Trenzalore’, she fears the worst. Jenny then cries out that someone has killed her. River makes everybody wake up, just as the Whisper Men call out that the Doctor’s friends will be lost forever unless he goes to Trenzalore.
In present day London, the Doctor hears Clara’s account and gets emotional explaining that Trenzalore is where his final resting place is located. Fearing for his friends, the Doctor takes Clara to Trenzalore where they find a massive graveyard (the site of the Time Lord’s final battle), a future Tardis (that has grown to gigantic proportions) and River’s headstone. When the Whisper Men approach, River – who is still mentally linked to Clara – tells her that her headstone is a secret entrance to the Doctor’s Tardis tomb. While fleeing the Whisper Men, Clara learns that River was the Doctor’s wife.
At the Doctor’s tomb, Strax revives Jenny just as Dr Simeon (Richard E Grant) arrives with the Whisper Men. Vastra deduces that Simeon is actually the Great Intelligence, who informs her the Doctor has the blood of 10 billion on his hands following a war in his final days. Back in the catacombs, Clara learns River died while trying to save the Doctor, and he stored her memory in a database. The fact he has never said goodbye to has kept her ‘alive’. With the Whisper Men closing in, Clara’s memories of climbing through a wrecked Tardis and of the Doctor asking her about her previous lives return.
At the tomb, the Great Intelligence threatens to kills the Doctor’s companions unless he opens the door to the Tardis using a word that is known only to him: his name. The Doctor refuses, but an unseen River says his name to save him uttering it. Inside shines a beautiful light. But it is actually the scar tissue of the Doctor’s journeys through time and space – from Gallifrey to Trenzalore. The Great Intelligence enters this tear in the fabric of the universe and begins to rewrite the Doctor’s timeline. Realising why the Doctor met her in Victorian London and on board the Dalek asylum, Clara steps into the wound and becomes 1000 lives in 1000 places in order save the Doctor. The Doctor then gathers his strength and bids River goodbye with one final kiss before stepping into the wound to rescue Clara.
Crossing into his own time stream, the Doctor successfully locates Clara and they depart, but not before catching sight of one of the Doctor’s incarnations that has yet to be. The figure turns around to reveal an older Doctor (John Hurt).