In “Day of the Doctor”-three incarnations of the Doctor helped UNIT negotiate a peace with the Zygon race, a group of shape-shifting aliens who have wanted to conquer the Earth, since their own planet had gone extinct.
The personification of this treaty was UNIT’s scientist Osgood, a fangirl of the Doctor, who was duplicated by the Zygons. Both the human original and her Zygon doppleganger served to uphold that treaty as it’s personification. They were ‘sisters’, in a sense. The Doctor entrusted them with a device called the “Osgood box” should the treaty break.
And then, one was killed by Missy, the female incarnation of the Master.
Now Osgood, who has left UNIT since(It’s not revealed whether the human or Zygon was killed by Missy) has been kidnapped by a splinter group of Zygons in New Mexico who want war, although the majority of Zygons just want to be left in peace.
The Doctor is then summoned by UNIT to help out. He sends Kate Stewart to Truth or Consequences-the town where Osgood was captured from-while the Doctor himself goes after Osgood.
He’s able to do so, and capture a Zygon in the process. The Doctor tries to figure out their plans.
Meanwhile, Clara is unfortunately replaced by a Zygon-who takes her form and calls herself Bonnie-and then is about to take out the Doctor. Kate finds herself trapped by Zygons as well.
The Doctor and Osgood escape Bonnie’s attempt, due to Clara’s mental imprint-despite being in a Zygon pod for safekeeping-being able to influence Bonnie to miss.
The Doctor and Osgood-following Clara’s clues sent using her influence on Bonnie-are able to figure out what she’s planning-she’s going for the Osgood box, intending to use it as a weapon. The Osgood box as it turns out is located in UNIT’s black archive, where the treaty first took place. Eventually, they all converge there, and it turns out there are two boxes. One, pressed by Bonnie, will remove all the Zygon’s disguises, causing panic among the world, as many Zygons have attempted to fit in using human disguises and only want peace. Another-pressed by Kate-will kill all the Zygons will a deadly gas.
The Doctor gives an impassioned speech, about the decisions he had to make in the time war, and what could happen if either of them pushes the button. Eventually, they both realize the errors of their ways. Turns out there was actually nothing in the boxes, anyway.
Resolving the crisis and with the Splinter Zygons called off, Bonnie switches from Clara to another ‘sister’ of Osgood, once again being a symbol for peace between humans and Zygons.
Next up there’s a weird “found footage” adventure in which the Doctor and Clara arrive on a spaceship, where a group of soldiers face off against mysterious ‘sandmen’ monsters.
Turns out these “sandmen” are in fact semi-sentient collections of eye dust created by a technology that is able to compress a month’s worth of sleep into five minutes.
Although the Doctor and Clara escape-although the Doctor is suspicious about the outcome of events, it’s known that the sand monsters intend to reproduce using a transmitted signal, which is in part sent by the “found footage” that the episode is comprised from. Oops!