The Doctor has returned to his home planet of Gallifrey. But he’s not happy-Clara is dead, and he’s been stuck in his own confession dial in a time loop for billions of years. Now that he’s out, he’s letting his displeasure be known.
The Doctor returns to the barn, possibly his home-and is greeted by other Gallifreyans (possibly his relatives) with soup and hospitality. However, the Time Lords-still led by Rassilon (Although he’s no longer Timothy Dalton) arrive.
Rassilon attempts to execute the Doctor, but the Time Lord military-because of the Doctor’s heroics during the time war-including saving their planet-relieve Rassilon and put the Doctor in his place.
It turns out, although Gallfrey has returned to the universe, it’s now temporally located near the end of time to hide from their enemies.They still want to know about the danger the hybrid poses to Gallifrey’s future, but the Doctor states that he needs Clara’s help to do so. They let him use a temporal extraction chamber to take her from the moment of her death.
This sort of leaves Clara in a time loop-although she can move and talk, her pulse and aging are frozen. The Doctor then turns on the Time Lords-it turns out he only intended to rescue Clara all along, and not really reveal anything about the hybrid.
Going down to the cloisters underneath Gallifrey’s citadel, the Doctor steals another TARDIS (as his own is still left on Earth) and tries to reverse the time loop. This TARDIS is in a configuration which resembles the original version of the Doctor’s, complete with round things. The Doctor has once again decided to go on the run from his own people in a TARDIS, although this time it’s to try to break the time loop so Clara can really live.
Unfortunately, it doesn’t seem to be working. The Doctor then decides to go to the point where Gallifrey is about to be consumed by the end of the universe, and runs into “Me” there, watching the universe burn in a nice comfy chair in the ruins of Gallifrey.
The two speculate on the nature of the hybrid. Is it “Me” herself, who has a mix of human genes and alien technology? Is it the Doctor and Clara? Is it the Doctor himself, who might be half-human because he goes to Earth so much? The Doctor then states he plans to erase Clara’s memory of him and leave her on Earth, to protect her both from the time lords-and because he’s gone too far to save her this time.
Clara however reverses his mind-wiping device, and it works on him instead. The Doctor then finds himself in Nevada, and he visits a local diner-with a waitress that resembles Clara. However, the Doctor-only having extremely vague and disassociated memories of her-doesn’t recognize her, but relates what he remembers anyway-and plays a sad song on his guitar.
As the Doctor plays his song, the waitress opens the door to the back of the diner, revealing it’s in fact the TARDIS that was stolen.
Clara and Me-now both pretty much immortal-than go on their own adventures throughout time and space, although one day Clara will have to return to Gallifrey to ‘die’ in the alley again.
As the Diner-TARDIS de-materializes, the Doctor’s own-recovered from London-shows up. Boarding it, he finds one last message from Clara-“Run you clever boy, and be a Doctor”-and he gets a brand new sonic screwdriver as well.
The Two TARDISes then pass one another in space as they both go on further adventures.