The Doctor finds himself captured by a group of humans living outside of the the Viryan’s shelters while Mila is captured by a group cooperating with them. Mila is then taken to the Viryan’s ship, where she is surprised to be confronted by a furious Charley, who is working for the Viryans since the Amethyst explosion. The Viryans have long since cured the disease Mila gave her, and millennia has passed for her in the service of the Viryans, luckily with most of that time spent in cryosleep. Charley has only asked one thing of the Viryans: that they help her reunite with the Doctor.
It turns out that the Viryans have been tracking down the viruses let loose across space and time by the Amethyst explosion. The human race has been contaminated with one, and the outbreak of madness that caused the collapse of human civilization was the unintended result of an attempt at a cure. With their cure attempts having failed, the Viryans haves decided that the only way to be completely rid of the virus is to wipe out humanity completely by and “cleanse” the Earth by dosing it in lethal radiation.
Using the TARDIS, the Doctor manages to stop this by encasing the signal to start the radiation bombardment in a time sphere, freezing it while he attempts to talk with the Viryans. Eventually, it is discovered that neither Charley or Mila is infected with the virus the Viryans are so concerned with and the Doctor realizes that exposure to particles produced by time travel must cure the virus. With the Viryan’s help, he expands the time sphere to include all of Earth and decides to take the planet back to before the Viryans discovered that the human race had been infected.
Meanwhile, Charley and Mila have both been trying to convince the Doctor that they’re the real Charlotte Pollard and the other is a fake. Charley finally tells the Doctor the truth about her origins, but it hardly matters. The Doctor decides that he can’t trust either of them, no matter who the real Charley is. He also tells them that this entire situation is likely the result of their paradoxical meddling in the timeline. They’re both kicked off the TARDIS while the Doctor tries to deal with the time sphere. Eventually, Charley and Mila come to an understanding and return to the TARDIS to try to help the Doctor. Mila sacrifices herself to save the Doctor. With the Viryan’s help, Charley has the Doctor’s memory changed so that he remembers all of his travels with her as being with Mila. A glum Doctor remembers Mila fondly while a heartbroken Charley continues to work with the Viryans.
- Anguished Declaration of Love:
- Just before a Heroic Sacrifice too.
- Charley gives one to the Doctor as well, but more towards his future incarnation.
- Acting for Two: India Fisher plays Charley and Mila-Charley.
- After the End
- Apocalypse How: Earth is leading up to a Class 2. The Viryans try to execute a Class 6. The TARDIS (unable to withstand the planet's radiation and the Viryan's attempt at planetary destruction) is nearly causing a Class X.
- Bittersweet Ending: The Doctor walks off thinking that instead of Charley he's been travelling with Mila (who has a different appearance) all this time, so that his mind is blank for his future incarnation, but not before Charley tells him all about her adventures so that he goes into a mindwipe willingly.
- Body Horror: Anybody touching the Time sphere.
- Book Ends: The opening and the ending are the same scene. The context is not clear until the second time around.
- Call-Back:
- Not the first time the Sixth Doctor had been on Earth with it looking radically different.
- The Doctor mentions having met the Viryans before and the results of the Daleks attempts at biological warfare.
- Charley mentions the console she knows looks wholly different.
- Doubles as a Call-Forward, as Charley recaps the events of the R-101, the disruption of time and the alleged true death the Doctor was supposed to go into.
- Earth All Along: The Doctor and Mila both find this out individually, that the post apocalyptic world they're on is Earth.
- False Memories: Charley has the Viryans do this to the Doctor so he doesn't remember her. He remembers her as being called Mila and looking different.
- Freudian Excuse: Mila justifies her sociopathic behaviour as a consequence of her time being tortured by the Daleks, and Charley has to concede that's a valid excuse.
- Godzilla Threshold: The genocides the Viryans execute.
- Gone Horribly Wrong: The "Madness" is the sideeffect of a cure for The Plague.
- Hate Plague: The Madness.
- Hit So Hard, the Calendar Felt It: Mila asks if it's 1930. Her reply is that nobody knows.
- Human Popsicle: Charley's been treated as one by the Viryans for millennia.
- "I Know You Are in There Somewhere" Fight: Driscoll tries this on a crowd with the Madness. It works, for a while.
- Immune to Bullets: The Viryans are being shot at, and calmly reply: "Please cease your hostile intentions."
- It's All About Me: Mila at one point provokes a riot against the Viyrans because she accuses the original Charley of being a clone they created rather than admit her own deception.
- Knight Templar: The Viryans are "treating" the human race for a 1.54 billion chance that sometime in the next 7 thousand millennia the dormant virus will become active. The Doctor is disgusted by this statement.
- Mythology Gag: The Doctor at one point quips: "You were expecting someone else?"
- Noodle Incident: Charley mentions her many missions with the Viryans and that they needed her on many occasions.
- Not Using the "Z" Word: When people don't take the Viryans' medication, they turn into raging madmen. Someone calls them zombies, and he gets corrected that they're still human beings.
- Oh, Crap!: Mila when she realizes the Viryans are involved, and know of her presence.
- Racial Face Blindness: An alien remarks to the Doctor he can't tell humans apart.
- The Slow Path: Charley, though thankfully with long periods spent in cytogenetic sleep, has spent millennia on the Viryans' ship.
- Title Drop: The second part starts off with one.
- Well-Intentioned Extremist: The Viryans are trying to rid the universe of the Amethyst viruses. They have “only” resorted to genocide 5 times.
