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?
Plot hole: In the middle of chasing the Doctor, Stor abandons the idea of controlling Gallifrey in favour of destroying it for no readily apparent reason.
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.
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.
Plot hole: Palmerdale and the others hear someone on the stairs. Skinsale opens the door and, despite Reuben being right in front of him, looks downstairs and calls out to the Doctor before turning and suddenly spotting the lumbering keeper.
Plot hole: Leela's decision to stay with Andred is very sudden. They barely speak during the serial.
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).
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