Plot hole: The damage caused by the shuttle crashing into the Bi-Al Foundation is seen BEFORE it actually happens.
Plot hole: The Doctor's clone is free of the virus - so why is Lowe's clone infected? Perhaps they infected him after cloning, in which case, why is Lowe cloned at all?
Factual error: Titan is depicted as a Moon-like landscape with no atmosphere. In actual fact, Titan has a nitrogen/argon atmosphere denser than Earth's, and a reddish-orange sky. This was detected almost thirty years before "The Invisible Enemy" was made, so somebody slipped up in doing their research.
Other mistake: When Marius injects the cloned Doctor and Leela into the real Doctor, the syringe is full of air, although the later graphic shows them in liquid.
Visible crew/equipment: In episode four, when the Doctor is congratulating himself on blowing up the Swarm, the shadow of a boom mike can be seen.
Plot hole: After the Doctor and Leela's clones fade, the camera pans to show Leela's knife. But since the knife was created in the cloning process, it should have faded out with Leela, the Doctor and their other personal items.
Continuity mistake: In episode three, the readout strip dangling from K-9's mouth shortens between when he shoots the infected crewman and shoot Leela.
Plot hole: Why doesn't Lowe simply shoot Leela the second her back is turned? Moreover, why does he take them to get medical help? It's made clear that the virus has everything it needs on Titan.
Visible crew/equipment: In the first scene of episode two, as the Doctor collapses on the ground, a person can be seen moving in the back of the set.
Revealing mistake: The knife that Leela kills Meeker with is very obviously loosely attached to his clothes. It wobbles back and forth after he falls.
Revealing mistake: In episode 3, the section of wall K-9 knocks down is obviously precut, complete with debris on the floor.
Continuity mistake: Lowe's "frozen" makeup changes between when he emerges from the freezer and when Leela brings him a cup of coffee.
Revealing mistake: When K-9 shoots one of the infected men, the blast beam appears to come out of his eyes, then moves down to his snout as the camera moves.
Plot hole: The Nucleus of the Swarm is referred to on numerous occasions as being a virus. A virus is the simplest form of life yet recognised and is made up of bundles of DNA wrapped in a coating of proteins. They reproduce by attaching themselves to other lifeforms and releasing their genes into an unsuspecting host cell. Viruses do NOT lay eggs. Nor do they resemble prawns.(It would be more accurate to describe the Nucleus of the Swarm as a protozoan. These are simple animal lifeforms radically more advanced than viruses, around a fifth of which are parasitic although not all cause disease).
Continuity mistake: The countdown clock in Marius' lab speeds up and slows down as needed for the plot.
Answer: It was never destroyed on-screen; it was intact at the end of the TV movie, and destroyed by the start of the 2005 series. It was destroyed in the novel "The Ancestor Cell," but in a completely different manner to what happened in the series.
DaveJB