In World Enough and Time, the Doctor is up against time itself, and it’s fairly safe to say he loses the battle.
The Doctor stumbles out of the TARDIS. He falls to his knees and the regeneration energy begins to glow. He lets out a scream, yelling no.
A shuttle is heading for a black hole, and the Doctor hears the distress call. With his newfound trust and a quiver of hope for Missy, he decides to see how she does as the hero. However, quickly after they arrive on the ship, an alarm goes off. A man comes out, holding a gun, demanding where the human is.
Flashback
The Doctor tells Bill about his idea: pick a scenario, put Missy in charge. Bill and Nardole adamantly say they don’t want to, too afraid and untrusting of Missy. The Doctor assures them that he’ll be monitoring, and Bill agrees on one condition: he promises she doesn’t get killed.
The Doctor tries to explain, through multiple scenes, that Missy is the only person “remotely like him”. He calls her his man crush, praises everything she was as a child, and explains their pact as students.
Flash forward
Now in the future, the gun points at Bill as the Doctor tries to talk him out of it. A hole blasts through Bill’s chest, killing her. Unidentifiable people come out of the elevators, saying they can fix her, taking her away. The Doctor leaves a message in her subconscious. Wait for me.
Bill wakes up from surgery and is now in a hospital with a metal box for a heart. Walking around, she finds other patients in rooms, some repeating the word “pain”, and one even saying “kill me”. She meets Razor, a man who works in the hospital. He explains that the bottom of the ship moves much faster than the top. So while Bill has been sleeping for months, it’s only been a couple minutes for the Doctor, Missy, and Nardole.
As time moves on, Bill becomes close to Razor, all while watching the Doctor on a screen he’s set up. She begins to work for the hospital as well, cleaning up floors. No one will tell her what’s really going on, or even where the lifts are. Razor only explains that life on this space station is not safe since they’ve been there for so long (despite the top of the ship only saying two days), and they need Plan Exodus.
Finally, the Doctor and Missy make it to the bottom floor, and Missy tries to find out more about this mysterious shuttle. She finds out the spaceship is from Mondas, Earth’s twin planet where the Cybermen were first from. Razor comes up to her. He takes a special interest in her, asking her if she remembers being here before.
The shocking twist
Razor comes up to her. He takes a special interest in her, trying to get her attention, asking her if she remembers being here before. It’s revealed that Razor is actually John Simm’s Master in disguise, worried about Missy becoming good. He’s worried about his future.
The Doctor comes back to find Missy gone, and begins looking for Bill. What he finds is a Mondasian Cyberman. He begs the Cyberman to tell him where Bill is. It is Bill. Bill was turned into a Cyberman.
The Masters emerge (in what is most likely one of the most iconic scenes of Doctor Who). They’re now planning the genesis of the Cybermen.
"BILL: I. Waited. For. You."
Next: 5 of Missy's Best Moments on Doctor Who (so far)