The Doctor walks into what look like a diner from the 1950s. Clara is a waitress behind the counter, though she doesn’t seem to recognize the Doctor. The Doctor says he doesn’t have any money, but offers to play his electric guitar. He plugs the guitar into sonic sunglasses. They talk about travelling and the Doctor strums his guitar. She asks if it’s a sad song. The Doctor says nothing is sad until it’s over. He tells her the name of the song is “Clara.” She asks him to tell her about Clara.
The Doctor walks the red planet of Gallifrey. He comes to a modest building.
The President asks the General if all the bells are ringing. Gastron reports that the Cloister Wraiths are active and all the bells are ringing. This is a sign of great danger. Ohila, backed by the Sisterhood of Karn, says the Doctor has come back to the beginning,
The Doctor looks around a stable. A woman finds him there and prattles on until she recognizes him. She warns the Doctor that they’ll kill him
The woman serves the Doctor a bowl of soup outside, where crowd has gathered. Before the Doctor can take the first bite, Gastron arrives in an armed ship and orders everyone to step away from the Doctor. Gastron then orders the Doctor to return with him to the Capitol. The Doctor draws a literal line in the sand and returns to his soup. The President, watching remotely, wonders what his plan is. They decide that words are the Doctor’s weapons, and they should be there’s as well.
The General, backed by an armed contingent, arrives at the Doctor’s home. He tries to be polite, but the Doctor simply goes back inside. A diplomatic envoy fails similarly. The President asks Ohila what if the Doctor wants revenge. Ohila says the Doctor doesn’t blame Gallifrey for the Time War, he just blames the President. The President himself is the next to visit the Doctor, backed by the General and another armed contingent. The President offers the Doctor his hand. The Doctor drops the confession dial in front of him and orders the President off the Doctor’s planet. The President insists that they had to know about the Hybrid and what the Doctor knows. The Doctor simply orders him away again. The President orders the soldiers to fire at the Doctor. The General tries to talk the President down, reminding him that the Doctor is considered a war hero. The President persists, and turns his back as the soldiers fire their weapons.
Back in the diner, Clara comments on how the Doctor likes a cliffhanger.
Back on Gallifrey, every single one of the soldiers missed their shot. The President demands Gastron explain. Gastron tells the President an old saying about the the “Doctor of War” from the Time Wars. He’s the first to cross over to the Doctor’s side, and the others follow.
At the diner, Clara asks if this is a story, or if it really happened. The Doctor says every story ever told really happened.
Ships arrive, and the President thinks the General called for reinforcements. It turns out the Doctor is the one who called them in. The General tells the President to get off the Doctor’s planet.
The President heads off of Gallifrey. The General wonders if the Doctor went a little far, but the Doctor says he’s only just started and that the High Council is on the next ship.
Ohila finds the Doctor observing the Cloister Wraiths and wonders about his motivations for sending the President away.
The Doctor meets with the General and the Sisterhood of Karn to find out what they know about the Hybrid. They tell him that the Hybrid supposed to be a cross between two warrior races, Dalek and Time Lord, and will stand in the ruins of Gallifrey. The Doctor asks for the use of an Extraction Chamber to talk to an old friend.
Back on Trap Street, time stops just before the raven plunges into Clara. The Doctor reaches his hand out from a bright door in reality and says he can save her.
Clara walks through, into the Extraction Chamber. Clara says she should be dead, and the Doctor tells her to forget it, it doesn’t matter. Clara is very confused, so the Doctor fills her in. The General says they only have a few moments with her. The General asks about the Hybrid, but there’s a ringing in Clara’s ear. The General tells the Doctor to tell her. He tells Clara that her physical processes have been frozen in time. The General explains that she died billions of years ago, and once they’re done talking to her she will be returned to the moment of her death. The Doctor punches the General and takes his gun. The General tries to talk him down, reminding him that he could fracture time. Clara tells the Doctor she doesn’t want this. The Doctor asks which regeneration the General is on. He says tenth. They wish each other luck and the Doctor fires. The Doctor takes something from the Chamber, and takes off with Clara, and the regenerated General is joined by Gastron and Ohila. The Doctor takes Clara to the Cloisters, where the Cloister Wraiths guard the Matrix.
At the diner, Clara asks what the Doctor took. He says to keep Clara safe, he had to erase some of her memories, specifically those involving him.
The General orders every available man to guard the Cloisters. Gastron says no one has ever made it out of the Cloisters, but Ohila says that’s not quite true.
The Doctor and Clara come across a Dalek who is trapped in the Cloister, a remnant of the Cloister War. Clara comes across some Weeping Angels and a Cyberman. The Doctor pulls her away and says they must be close to the Matrix Database. The Doctor explains that when a Time Lord dies their mind and memory are uploaded to the Matrix Database, to create prophecies and warn of oncoming danger. They’ve found a possible secret exit and the Doctor is piecing together the code, and telling Clara of how he escaped the first time. Clara notices that the Doctor won’t look her in the mind, and he tells her a little bit of what happened. She asks what happened to his velvet coat that was so “Doctory.” He says he can’t be the Doctor all the time. The Doctor finishes telling her the rest of the story as the General and Ohila arrive. The Doctor hints that he may not know anything about the Hybrid, but is playing the Time Lords to save Clara. Clara demands that they tell her how long the Doctor was in his Confession Dial. They tell her it was 4.5 billion years. Clara tells him that her time is up. She says people like the Doctor and herself should say things to one another, and she’s going to say them now.
The camera pans away, and when we come back Clara walks away from the Doctor. She tells the Time Lords that they’re hiding away at the end of time because they’re monsters and they’re hated. Ohila asks what Clara told the Doctor. The only part she reveals is that she told the Doctor they’d all be looking at her. The Doctor shows up with a fresh TARDIS and brings Clara inside. Ohila calls him out, calling him “boy.” She accuses him of breaking every oath and code he’s ever lived by, and giving Clara nothing but hope. He argues that the universe owes him this, and that hope is a good thing. He takes off, and the General asks where he’s running to. Ohila simply says “away.”
The TARDIS flies off. The Doctor tells Clara that he thinks she’s fine, and that now they just need to lose the Time Lords. Clara says she still has no pulse. The Doctor looks at the back of her neck, and the tattoo from Trap Street is still on the back of her neck. The Doctor asks if she trusts him, and she says not when he’s shouting. The Doctor says he’s taking them past the end of time, where the Time Lords won’t follow. She still doesn’t have a pulse. The Doctor is frustrated, saying this should have worked. There’s a knock at the door, a familiar four knocks. Clara goes to answer the door, but the Doctor says he does this alone.
The Doctor exits the TARDIS. Outside, he finds Ashildr sitting with a chess board. Ashildr tells the Doctor that Clara died billions of years ago, by her own choices, and it was sad and beautiful and that they have no right to change who she was. The Doctor disagrees. Ashildr brings up the Hybrid and says its time tell the truth. Inside the TARDIS, Clara uses the Sonic Sunglasses to eavesdrop. The Doctor theorizes that Ashildr is the Hybrid, half-human and half-mire. Ashildr suggests that may the Doctor is the Hybrid, secretly half-Time Lord and half-Human, and says that would explain why he spends so much time on Earth. Then she suggests that maybe the Hybrid is two people, Clara and the Doctor, and points out that it was Missy that brought them together. The Doctor revels his plant to bring Clara back to Earth and wipe his Clara’s memory of her using the Time Lord tech. Ashildr cautions that this might not be what Clara wants.
The Doctor bring Ashildr onto the TARDIS. The Doctor notices Clara isn’t surprised to see Ashildr, and Clara admits to having watched and listened. Clara tells him that he revered the polarity of the neural blocker. The Doctor says he is trying to keep her safe. Clara says she never asked or that, that these have been the best years of her life and that she’s entitled to keep them. The Doctor thinks for a minute, then admits that she is right, now and always. The Doctor says he’s not sure what she did to the neural blocker, but that one of them has to go. They both take hold of the neural blocker. They press the button together. A moment later, it drop from the Doctor’s hand and he drops to his knees. He gives her the last advice he can before falling over. Clara says she didn’t mean for this to happen, but the Doctor accepts that he went too far. He finally passes out.
The Doctor wakes in the desert, unsure of how he got there. A man stands over him, and the man says that Clara asked him to watch over the Doctor. The Doctor has no idea who Clara is.
In the diner, the Doctor finishes his tale, telling Clara of how you can recreate something that’s missing by examining the space it left. He remembers their adventures, and has her name, but doesn’t know what she looks like. Clara says she could be anyone, even her. The Doctor says he’s positive that if he met her again, he would know. Clara hides tears, and asks about the TARDIS. The Doctor says he hasn’t been able to find it. It was moved from London. Clara exits the diner’s back door, into the TARDIS from Gallifrey where Ashildr is waiting. They take off together, and the diner disappears, leaving the Doctor’s TARDIS behind.
Ashildr says the chameleon circuit is stuck, that their TARDIS may be stuck as a diner forever. Clara says she’s still stuck between heartbeats, which her means her death is still a fixed point in time. She figures the Time Lords can send her back, so they head for Gallifrey…the long way around.
The Doctor enters the TARDIS. He finds a message on the chalk board: “RUN YOU CLEVER BOY…AND BE A DOCTOR.” There’s a velvet coat waiting for him. A new sonic screwdriver pops out of the TARDIS console. The Doctor snaps the TARDIS door closed, and the TARDIS takes off, crossing the other in the sies of space.