The Doctor and Sam are on Silhouette Island in the Seychelles, where the Doctor is trying to decide whether he should take Sam back to London or let her continue travelling with him. Before he can decide, he and Sam encounter a Rhiptogan, a shape-shifting alien fugitive who is searching the beach for missing parts from his damaged spaceship. The fugitive, Lirpa, flees with the TARDIS key, and the Doctor is forced to pursue him -- but he is followed by a Rhiptogan bounty hunter, Ruduse, who kills Lirpa by throwing him into a tidal pool. The seawater melts away Lirpa's body, and Ruduse takes his head as a trophy. Meanwhile, Sam locates the fugitives' ship, where she is captured by the other fugitive, Ladeeth -- and is poisoned by the alien plants growing around the ship's entrance. Ruduse arrives and fights Ladeeth, seriously injuring him; but the Doctor then arrives with a bucket of seawater and threatens to kill her unless she lets Sam go. Ruduse, however, realizes from Sam's disappointment and the Doctor's subsequent reaction that the Doctor is bluffing, and since Sam had mentioned that the Doctor had run away from his own people, Ruduse decides to capture him as well for the bounty. Sam, however, throws the bucket of seawater into the damaged shuttle's controls, and Ladeeth uses the last of his strength to hold back Ruduse as the Doctor and Sam escape. Moments later, the alien ship explodes. The Doctor takes Sam back to the TARDIS and cures her, and agrees to let her accompany him on his travels after all.

Time-Placement: The first trip of Sam in the TARDIS, so it’s set right after The Eight Doctors.

Continuity Note: After this adventure, the Doctor drops Sam off at a Greenpeace rally for three years by his point of view but only an hour for Sam, during which time the Doctor travels with Stacy and Ssard (Radio Time Strip), meets Benny (The Dying Days) and possibibly starts travelling with Charley (Storm Warning).

The TARDIS is brought down in a black void, and Sam and the Doctor emerge to find themselves in a lifeless walled environment which the Doctor seems to find strangely familiar. As they explore further, the area slowly becomes illuminated, revealing the twisted, distorted statues of people in agony. Just as the Doctor realizes that they've landed in an ancient, dying TARDIS, Sam is trapped in a temporal stasis field and the Doctor is assaulted by insane telepathic voices which try to burrow into his mind. As he tries to fight them off he receives a telepathic message from himself just a few hours in the future, warning him that his attackers are insane Time Lords who converted themselves into electrochemical impulses in an experiment to follow the temporal psychic pathways of Time Lords. They learned that they could manipulate the past of their subject, but when they did so and then tried to exit their host, a loose thread caused his entire timeline to unravel and they were trapped in this form, forced to move from host to host. They were trapped in this dying TARDIS when its owner suffered a brain seizure, and have gone mad over the millenia; now that they have captured the Doctor, however, they intend to possess him, go back along his timeline and return to Gallifrey. But when they depart his body they will kill him in his past, unravelling the causal nexus. The Doctor allows them into his body and monitors them as they travel back along his timeline -- and traps them within his mind at the moment of his first regeneration, explaining to Sam that it's as though they're beneath a cut which has healed over.

Time-Placement: The only reference to another work which I can see is the "Jones-Richter Scale" of trouble, which was first introduced in the early chapters of Genocide. Sam also notes that things often seem to be going wrong with the TARDIS, likely a reference to the events in that book.