Spoilers for Series 9 ahead!
One of the plot threads of the 50th Anniversary “The Day of the Doctor” was the Zygon invasion that started with Queen Elizabeth I in 1562. When Kate Stewart discovered UNIT was compromised, she was prepared to detonate a nuclear bomb to destroy London and take out the Zygons. The Doctors were able to facilitate a peace treaty by momentarily wiping everyone’s memory so they couldn’t remember if they were Human or Zygon.
The Series 9 Zygon two parter is a followup to the 50th Anniversary special. As a result of the treaty, twenty million Zygons have been living as disguised humans on Earth. Vital to maintaining the peace is Osgood, who bonded with her Zygon double as a sister. But the peace is threatened when Missy kills Osgood. The surviving Osgood is left to grieve, while a splinter group of Zygons who are unhappy with the status quo revolt.
The Doctor arrives in London after the splinter group of Zygons have captured Osgood. He tries to contact the Zygons by chasing down two school girls in a playground who are Zygon commanders. Unfortunately the rebel group captures them and broadcasts their intent to start a war. The Doctor and UNIT rescue Osgood while Kate Stewart travels to Truth or Consequences New Mexico to investigate the splinter Zygons. Early on in the invasion, Clara is captured and cloned by the Zygons. Her doppelganger calls herself Bonnie. For most of the first part, she operates undercover, but reveals her hand during the episode’s cliffhanger.
During “The Zygon Inversion” The Doctor and Osgood attempt to foil Bonnie and the Zygons’ plans and restore the peace. Clara finds herself trapped in a version of her apartment where the door and windows open to brick walls and the TV has one channel showing events as they unfold. Clara is able to wrestle a little control from Bonnie and forces her to text The Doctor to let him know she’s alive. The Doctor video calls her and recognizes the subtle clues like winks Clara leaves for him.
Bonnie forces Clara to tell her the location of the Osgood Box, a device the Doctor left with the two Osgoods to help keep the peace. It’s kept at UNIT’s Black Archive beneath the Tower of London. She wants the Osgood Box so she can control the human Zygon conflict. Bonnie, Osgood, The Doctor and Kate Stewart all arrive at the Black Archive where they discover there’s two Osgood Boxes, each with a doomsday scenario. One box will either release a gas to destroy the Zygons or detonate the nuclear warheads underneath the Black Archive, while the other box would either expose the Zygons or make their human forms permanent.
Neither box has a label as Bonnie picks one, Kate picks the other. Both are ready to push a button when the Doctor makes an impassioned speech about the consequences of war. He manages to persuade both Bonnie and Kate to back off. For good measure, The Doctor wipes the memories of Kate and everyone else in the room except for Bonnie. She calls off the splinter group. Bonnie can’t remain as Clara so she becomes another Osgood doppelganger. The two continue their mission of maintaining the human Zygon peace.
Series 9 was packed with plenty of great episodes. I really liked how “The Zygon Invasion/Inversion” followed up on the Zygon plot of “The Day of the Doctor.” Looking back at the 50th Anniversary, it was hard to remember as the War Doctor/Time War plot overshadowed the Zygons. It’s always refreshing to see consequences to the Doctor’s actions. Capaldi’s speech at the end of “The Zygon Inversion” is one of the stand out moments of Series 9 and will most likely be included in any Greatest Hits Twelfth Doctor compilation.