The Doctor travels around the universe for years trying to find a cure while Charley is comatose in the Zero Room. He finds himself at the Amethyst Viral Containment Station, where he encounters a group of time traveling Daleks seeking to steal the viruses and locate a mysterious individual who they call “Patient Zero.” The Daleks are opposed by a powerful group of aliens called the Viryans, who have already pledged to destroy all traces of the viruses.
Meanwhile, Charley wakes up and finds that she isn’t alone on the TARDIS. She meets a mysterious woman named Mila, who fades in and out of existence. Mila tells Charley that she is a former Dalek prisoner and her condition is a result of Dalek experiments to try to create a disease that would turn the entire universe into Daleks. Mila herself is the “Patient Zero” the Daleks are looking for. After escaping the Daleks, she found herself on the TARDIS during the events of The Chase and has been living on the TARDIS ever since, unable to be seen or to communicate. Mila has come to greatly admire the Doctor and wants nothing more than to be like one of the companions she has spent countless years watching.
Charley is not protected from Mila’s virus by the TARDIS like all previous companions. Over the course of the story Mila begins to transform into Charley while Charley herself fades away. Eventually, Mila replaces Charley entirely. An almost completely intangible Charley is captured by the Viryans while the Doctor, with the help of a disguised Mila, destroy the base with a temporal explosion, becoming trapped in it themselves as they attempt to flee in the TARDIS. Unfortunately, the destruction is not complete enough to stop the release of countless dangerous viruses across time and space.
- A Fate Worse Than Death: Mila (And Charley) consider being turned into a Dalek is worse.
- And I Must Scream: Mila was stuck in the TARDIS since The Chase. Now even with the loose continuity of how old the Doctor is, how many years have passed since his First incarnation and his current?
- Assimilation Plot: What set the entire plot of, with the Daleks as the ones who would assimilate .
- Call-Back: Mila hid on a Dalek Time Ship pursuing the Doctor when he was an old man. She mentions the events of the Tenth Planet, a looooong scarf and him having various companions throughout the years.
- Continuity Porn: While she's in Charley's body she mentions several of the Doctor's adventures, like his defeat of their invasion of Earth, defeating them in Vulcan, their Time Destructor on Kembel and when he induced them with the human factor.
- The Zero Room is used to sustain Charley.
- Mila mentions the Doctor that he used to have long, white hair and a mop.
- Call-Back: When the Dalek Time Controller is contacted, several sound clips from various Dalek audios are heard, with a soundbyte from the Fifth Doctor and the Sixth Doctor.
- Call-Forward: Then soundbytes are heard from the Seventh Doctor and the encounter between the Eighth when he first met them with Charley.
- Cliffhanger: The audio play ends with the Doctor and Mila in Charley's body trapped in a temporal explosion, uncertain of their fate, and uncertain if Charley would ever reassert control of herself.
- Conqueror from the Future: The Daleks.
- Decontamination Chamber: The Doctor is hit by a blast when he materializes in the station.
- Determinator: The Doctor is this to Charley. He is willing to let Daleks proceed with their plan if he can keep her alive.
- The Dreaded: The Viyrans seem to be this.
- Fusion Dance: Fratalin can merge with his "familiars".
- Grand Theft Me: Mila successfully pulls this on Charley.
- Have We Met Yet?: At the very least, the Dalek Time controller knows of the Seventh and Eighth Doctors.
- It gets more complicated. According to "The Dalek Generation" the first Doctor it met was the Eleventh.
- Heroic Sacrifice: Fratalin stays behind to help Mila (as Charley) and the Doctor escape.
- Hive Mind: The Fratalin have a form of this, being a single being consisting out of several gigantic cellular creatures. They can link up and share info.
- Hourglass Plot: Mila starts out barely in existence, until she slowly starts taking over Charley, and the reverse happens to Charley.
- I Lied: The Doctor pulls one on the Daleks.
- Loony Fan: Mila certainly seems like this to the Doctor, desperate to be a companion.
- Me's a Crowd: Mila, as Patient Zero, was bombarded with a genetic virus which turned other creatures into her.
- The Plague: Amethyst contains many, which is what the Daleks want.
- Rip Van Winkle: Between the opening and Charley waking up again, years have passed.
- Single-Biome Planet: The Fratalin station is in orbit of a "Lava planet".
- Space Station: See above trope.
- Stable Time Loop: The viruses were spread through time by a temporal explosion, caused by the Daleks when they traced the viruses back to the Station. The Dalek Time Controller works this out and orders the Daleks to let the explosion happen.
- Stompy Mooks: The Viyrans.
- Time Stands Still: The Daleks employ technology to freeze an explosion of the Space Station because they fear defeat.
- Timey-Wimey Ball: It's unknown when the Daleks experimented on Mila, and they shunted her back (by accident) into the TARDIS, Charley coming from the future into the Doctor's past, all leaving the current situation.
- Trauma-Induced Amnesia: Mila can't remember who she was before she was a prisoner of the Daleks.
- Villainous Rescue: The Doctor is saved from being jettisoned into a lava planet by the Daleks.
- The Virus: What Mila has. The Daleks want it to turn other species into Daleks.
- The Worm That Walks: Fratalin and his 799 Familiars.
- You Can't Fight Fate: Why the Dalek Time Controller doesn't have the Doctor exterminated. It doesn't want to disrupt the Web of Time.
