The Doctor believes that someone from the orbiting ship has pretended to be him to board the TARDIS. The Brigadier, however, is unable to tell him what happened. The Doctor finds Turlough's crystal and sets off to stop him from leaving them behind.
Mawdryn continues to pretend to be the Doctor, telling the Doctor's companions that the transmat altered his DNA. He wants to return to his ship. When he doesn't recall Turlough, the girls are suspicious. But Mawdryn appeals to them for mercy.
The Doctor uses the transmat to signal backward in time to the TARDIS. He asks the Brigadier if he travelled with Tegan and Nyssa — worrying that the two Brigadiers could meet and short out the time differential. But before the TARDIS can arrive, the signal beacon explodes. The Brigadier, however, has Tegan's TARDIS-tracking device in his cottage.
The TARDIS arrives on the ship. Tegan still suspects Mawdryn, but his obvious suffering persuades them to let him out. Mawdryn staggers through the ship and calls out to his crew.
The Doctor pilots the transmat capsule to the ship with the Brigadier and Turlough. He sends Turlough to the TARDIS while he and the Brigadier serach the ship. They find a room filled with sophisticated machinery. It is designed to help Time Lords regenerate and must have been stolen from Gallifrey. They realize there are at least eight creatures on the ship.
The Guardian tells Turlough the Doctor is now doomed. He has Turlough open a secret panel, which reveals the other seven mutants. They stagger out in search of Mawdryn.
Mawdryn reaches the regeneration room where the Brigadier, thinking him the injured Doctor, connects him to the machine. Mawdryn explains that the system merely stabilizes his anatomy — he can not die.
The Doctor goes to the TARDIS and realizes that the Brigadier is on the ship in two forms. The Doctor then confronts Mawdryn, who explains they stole the machine to try to regenerate. Instead, it induced mutation so horrible they were exiled. The ship periodically approached a planet so that they can search for help. But there is no help — unless the Doctor is willing to give it to them.
They beg for the Doctor's help to die. But he tells Tegan doing so would mean the end of him as a Time Lord…