Clara wakes in her apartment, but realizes she's still in a dream state inside the cocoon.
From the television set, she learns of the Doctor's predicament. However, since Bonnie is her duplicate she's able to influence the Zygon into misfiring. Unfortunately, the second missile hits its target. The Doctor and Osgood manage to parachute to safety.
Bonnie then stalks another shapeshifter, forcing his Zygon form to reveal itself. She broadcasts his transformation on the internet, then goes in search of the Osgood box.
The Doctor and Osgood receive a text message from Clara, "I'm awake" it reads. Osgood theorizes that Clara is not dead and in a pod somewhere fighting for control. She Facetimes Bonnie/Zygella and the Doctor notices her wink, which means Clara is communicating. He determines the location of her pod and warns Clara not to tell Zygella what the Osgood box is.
Naturally, this leads Bonnie/Zygella directly to Clara's pod for questioning. Using their linked hearts, the Zygon determines whether or not Clara is lying. She threatens to kill her and learns the Osgood box is at UNIT HQ in the Black Archive. Since Clara has access to the facility, that means Zygella does as well. The alien makes her way there, along with Clara in her Zygon pod.
Following the last location of Bonnie's phone, the Doctor and Osgood chat with the shapeshifter exposed online. The man informs them that a Zygon commander turned him back. "There's their plan. Unmask everyone. Provoke fear and paranoia. Provoke a war!" the Doctor says.
Kate (posing as a Zygon) arrives and offers to take the Doctor to Clara's pod. It doesn't take long for them to realize Clara is missing.
Meanwhile, Bonnie/Zygella along with Clara in her pod arrive at UNIT HQ. The Zygon soon realizes there are two Osgood boxes.
When Kate contacts Zygella, the Zygon informs her there are two boxes and asks her to bring the Doctor immediately.
Threatening Clara's life, the Doctor tells Zygella the blue box normalizes the Zygons. She presses the main button and the lid opens to reveal a set of "truth" or "consequences" buttons. The alien is even more frustrated at this point.
At the Black Archive, the Doctor pleads with Zygella to allow him to take the boxes away and let the cease fire stand. She refuses, so Kate moves to the red box. If the Zygon will not listen to reason, she will be forced to end them.
While the Zygon complains of the unfairness of their current situation, the Doctor works to convince her to break the cycle. "The only way anyone can live in peace, is if they're prepared to forgive" he tells her.
Moved by the Doctor's words and realizing the boxes are empty, Bonnie/Zygella agrees to end the conflict.
A memory wipe later, only Zygella remembers exactly what took place and the cease fire is reinstated.
Though the Doctor offers Osgood an opportunity to travel with him, she politely declines. Zygella has taken on Osgood's face and the two will protect the peace treaty. The pair decide to go for ice creams and then back to work.
Inside the TARDIS, Clara questions the Doctor about her death. "Longest month of my life" he tells her very seriously.