The Doctor used the TARDIS to travel to the DEEP in order to stop Lee's genetic experiments after he suspected them before getting confirmation with the unwitting help of Professor Eric Vollmer, Lee's experiments had already been banned by half a dozen international treaties. When the TARDIS arrived in the DEEP, Flint sent Lee to investigate, and found the Doctor locking the door. After taking the key from the Doctor, Lee tried to unlock the door with the key but it wouldn't work, and subsequently gave it to Flint.
The Doctor was cut off from his TARDIS when he was forced to escape the DEEP when Flint activated the base's auto-destruct sequence. He tried to find the TARDIS key when Flint was badly injured by Vollmer, who had been mutated by Lee's genetic mutagen, but the general had already hidden it elsewhere on the base and refused to tell the Doctor where he had hidden it.
When the Doctor returned to complete his self-appointed task to destroy Lee's work and make sure no-one on the surface tried to duplicate it, Hoskins found the TARDIS only to be confronted by the Doctor, who threatened him. After changing the subject, Hoskins enquired about the box and asked the Doctor if it was worth anything. Amused, the Doctor stated the police boxes had been decommissioned "some time ago." Puzzled, Hoskins wondered what it was doing in the base. The Doctor admitted it was his, surprising Hoskins, but he refused to add any more details.
When General Flint revealed he had survived the whole time, the Doctor referred to the TARDIS by its true name during the revelation of the truth of what had happened to Volmer to Ruth, Vollmer's daughter. The Doctor admitted that he planned to leave in the TARDIS following the destruction of the DEEP and the destruction of Lee's remaining work, leaving Ruth behind with "another mystery" to haunt her.
Flint showed the TARDIS key and the Doctor tried desperately to get it back, but the general force-fed it down the Doctor's throat in revenge for what had happened 27 years previously. During the struggle, the Doctor's neck snapped, and he regenerated, only to be shot by Ruth. (AUDIO: Full Fathom Five)