The Doctor’s certainly been thrown for a loop. The Master is back, but now as “Missy”, a female incarnation. Plus, the mysterious 3W organization, harvesting souls and bodies, has turned out to be an army of Cybermen under her control.
However, UNIT-along with Kate and Osgood-is able to quickly mobilize and capture Missy and fend off some of the Cybermen-but several launch from St. Paul’s cathedral, where Missy says they’re going to launch a storm of nanomachines which will convert all the dead into Cybermen.
Clara remains trapped in 3W, but is saved by Danny-who unfortunately, has been cyberconverted. However, despite his conversion, he remains in love with Clara.
The Doctor meanwhile, is given control of UNIT, but is unsure of what to do. Missy however, using her powers of hypnosis on her guards, is able to escape, and unfortunately kills Osgood. She also reveals that the Doctor having a companion such as Clara was her design-it was her who gave Clara his phone number back in his last incarnation, so he would have an overly emotional companion.
The Doctor is able to escape the destruction by skydiving into the TARDIS, and reunites with Clara and Cyberdanny at a graveyard.
However they are soon met also by Missy. Missy’s plan is reveal-she plans to turn every human, alive or dead, into Cybermen using the Cyber-converting nanomachine clouds-and then give it to the Doctor to use as an army as a “birthday present”.
She wants this to prove that they’re not as different as he thinks they are-that he could use his new army to right every wrong. The Doctor is initially unsure what to do with Missy’s ‘present’-he’s still been grappling with a moral crisis. But then he sees Clara embracing with the Cyborg Danny. He realizes though, that he’s not perfect, he’s just an idiot with a box or screwdriver, he tries to help people-and he doesn’t need an army, he’s got his companions, who have compassion.
He then gives the controls for the Cyberarmy to Danny, who then orders the Cyberarmy to detonate and destroy the Cyber-converting clouds. Self-destructing, Danny dies, along with the rest of the Cyber-army; save one, a Cybermen formed out of Brigadier Lethbridge-Stuart, who saved his daughter and then appears to disintegrate his old nemesis-something even the Doctor and Clara can’t do despite what she’s done. The Doctor salutes his old friend, who then vanishes for parts unknown.
Clara and the Doctor then go their separate ways-The Doctor heading to where he believes Gallifrey may be, due to Missy telling him it’s back in the universe-unfortunately, there’s nothing there. Clara meanwhile tries to get Danny back from the nethersphere using one of Missy’s devices, where his mind returned, but he sends back a young boy instead who needs his family. Lying to each other that they’ve both found what they needed and sharing a hug, the Doctor and Clara appear to part ways…for now.