The one with a killer shrimp. Also, we meet a beloved tin dog.
A virus lurking in deep space infects the crew of an earth shuttle on its way to Titan. The infected humans kill the crew they are supposed to be relieving, except for one man, Lowe, whom they infect. They begin preparing the base for breeding. Meanwhile, the TARDIS has been invaded by the same virus, and the Doctor becomes the host for the Nucleus of the Swarm. After he attempts to kill "The Reject" Leela (who is immune), the Doctor realizes what's happening and puts himself into a self-induced coma to keep from being taken over completely. Leela, accompanied by Lowe, rushes him to the Bi-Al Foundation hospital asteroid using the TARDIS, where she hopes Professor Marius will be able to find a cure.
Professor Marius, a kind old genius, immediately realizes what's been going on. While Leela goes off to fight her attackers with the help of Marius' robot dog, K-9, the (still rapidly dying) Doctor asks Marius to make temporary clones of him and Leela. Lowe infects as many of the hospital staff as possible, and the cloned Doctor and Leela are shrunk down for a "Fantastic Voyage" Plot to try and destroy the virus by attacking it inside the Doctor's brain.
The short-lifespan clones expire before they can defeat the virus, but they drive the Nucleus out of the Doctor's brain, where it is expanded to human size. Lowe takes it back to Titan, to begin the breeding of a new giant shrimp virus super race, while Leela's decomposing clone corpse inside his brain gives the Doctor immunity to the virus. With the help of Professor Marius and K-9, the Doctor is able to isolate the immunity and synthesize a cure.
While Professor Marius treats the infected hospital staff, the travelers take the weaponized cure (and K-9) and head to Titan to finish off the virus. Leela knifes some people in the neck and keeps suggesting that the Doctor should just blow up the entire moon. He gives a grand spiel of not wanting to kill anyone, but eventually relents and blows up Titan. Professor Marius returns to Earth and gives K-9 to the Doctor as a souvenir.
- Affably Evil: The Nucleus holds no particular grudge against the Doctor, and admits that the Doctor would be perfectly within his rights to kill him... if he can.
- Asteroid Thicket: The episode begins in one, prompting one member of the relief crew to take their shuttle off auto-pilot.
- Body Horror: A space parasite lay eggs in the Doctor's brain which begins to passively alter his behaviour, making him go vulnerable, confused and Ax-Crazy. Less scary than it sounds, unfortunately.
- Break the Badass: When a space parasite lays its eggs in the Doctor's brain and mind controls him into being evil, as soon as he realises what has happened he is so scared he's almost panicking.
- Chekhov's Gun: The Doctor's antibodies.
- Cloning Blues: The Virus seems to try to induce this in the Clone Doctor, but he doesn't mind dying to save his own life.
- Detect Evil: Leela can "sense" the evil of the coming episode so strongly that she chews on the Doctor's scarf for comfort and forcibly prevents the Doctor from opening the TARDIS doors. Naturally, he ignores her.
- Distracted by My Own Sexy: Averted by Leela when she gets a look at her clone:Leela: "K9, "do I really look like that"?"K9: "Affirmative."Leela: (disapproving look)
- Double Meaning: The Doctor and Leela make an Accidental Pun while hunting down the nucleus:Doctor: "This is the mind-brain interface, Leela. That's the mind, and that's the brain. Two things entirely different but part of the same thing."Leela: "Oh, like the land and the sea."Doctor: "That's right, that's right." (smiling in approval)Leela: "It's very deep." (looking down into the abyss)Doctor: (unaware of this) "Yes. Sometimes, I don't quite understand it myself."
- Eternal English: Given the somewhat wobbly translation conventions of Doctor Who, this is always hard to say anything at all about. The exit sign on Titan clearly marked "EGGSIT", though, clearly suggests that they are using some version of English under a spelling reform in the 51st century.
- Repeated at the hospital (the Doctor is placed in the "ISOLAYSHUN" ward, among other things).
- Expendable Clone: The Doctor and Leela create "quick-clones" of themselves with the full memories and consciousness of the originals. The quick-clones have lifespans measured in hours, and the Doctor isn't terribly bothered about it.
- Face Full of Alien Wing-Wong: The Doctor's brain is infected by a pregnant microscopic shrimp.
- "Fantastic Voyage" Plot: At one point, the Fourth Doctor has himself and Leela cloned and shrunk down so he can be injected into his own brain, and fight the monster that's nesting inside it.
- Fighting from the Inside: The Doctor tries to resist the virus and succeeds in slowing it.
- Foreshadowing: At the very beginning of the episode, the Doctor compares humanity's explosion into the galaxy to a virus.
- Genetic Memory: The clones of the Doctor and Leela have the memories of their originals. K9 explains that this is because they are more like "biological photocopies" than proper clones, hence their shortened lifespans. Which does not in any satisfactory way explain how they cloned their clothes. Homaged much later on in "The Doctor's Daughter".
- Glad I Thought of It: Blowing up the Nucleus and its eggs:The Doctor: Good idea of mine, K-9, to blow them up.Leela: But it was my idea!The Doctor: Then you should be feeling very happy right now.
- Herr Doktor: Professor Marius.
- Hypnotic Eyes: Contact has been made.
- Informed Self-Diagnosis: An odd inversion in that the Doctor's self diagnosis confirms Professor Marius's analysis, rather than the other way around.
- Malevolent Masked Men: The infected shuttle crew have their space helmets when going to kill those on the base. On lifting the visors, we see how the Virus has altered them.
- Mega-Microbes: The miniaturized clones of Leela and the Doctor confront the virus inside the real Doctor's brain. Later, the virus is taken out of the Doctor and enlarged to human scale.
- Not Themselves: The Titan relief crew initially, then the Doctor. Leela can tell the difference instinctively.
- Our Monsters Are Weird: The Swarm is a sentient brain parasite that transmits itself across space through a flashing pulse of light. Witnessing this light pattern causes the Swarm to be created in your brain.
- Parrot Expo What: When the Doctor tries to explain things, Leela keeps repeating words she doesn't understand. Including 'parrot?'.
- Pig Latin: Professor Marius gives K-9 the order to 'kanayli' the infected.
- Puppeteer Parasite: The Nucleus and its ilk.
- Robot Buddy: K-9.
- Running Gag: As in "The Hand of Fear", Gallifrey is mistakenly believed to be in Ireland.
- Seeker White Blood Cells: While inside the Doctor's bodynote , the Doctor and Leela are attacked by white blood cells, but the Doctor uses a nearby nerve cluster to send them a fake message summoning them to a different part of the body. Now, this wouldn't work in a human body, where white blood cells just wander aimlessly and deal with whatever they happen to come across, but maybe a Time Lord's immune system works differently.
- Shrink Ray: The Doctor and Leela are shrunk with a shrink ray based on the same technology as lets the TARDIS be bigger on the inside, allowing a bit of handwaving about the issues of shrinking living things.
- Some of My Best Friends Are X: The Doctor, just before he adds that in large groups Humans Are Bastards.
- Techno Babble: More like medi-babble, but still.
- The Virus: The Nucleus.
- Visible Boom Mic: When the Doctor is congratulating himself on blowing up the Swarm, the shadow of a boom mike can be seen.
- Whole Plot Reference: To Fantastic Voyage.
- Wig, Dress, Accent: Leela disguises herself as an infectee with remarkably sophisticated face paint to gain access to the Doctor.