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The medical center mounts a defense against alien forces trying to take the comatose Doctor while clones of Leela and the Doctor go microscopic so they can hunt down the intelligent infection that's in his head.
The Doctor draws into himself, fighting the voice in his own head that's trying to take over his intelligence.
In trying to retrieve the clones from inside the Doctor, the alien virus is brought from the microbial world into the macro-world, and it's ready to spawn.