England, 1983: Brendon Public School. Turlough, a red-haired teen with an air of smug superiority, convinces the reluctant Ibbotson to take their math teacher's classic Humber car for a spin. Much to Ibbotson's horror, Turlough continues on beyond school property -- and is forced off the road by an oncoming car. Turlough is flung from the Humber and awakens to find himself floating above his unconscious body as school officials gather at the scene of the accident. A dark figure appears to Turlough and offers him the chance to leave Earth and return to his real home -- but only if Turlough kills the evil entity known as the Doctor. Turlough is hesitant to commit murder -- but as he begins to return to consciousness and the opportunity slips through his fingers, he agrees to do so. He awakens to find Dr Runciman tending to him, while his math teacher -- Alistair Gordon Lethbridge-Stewart, the former Brigadier of British UNIT -- angrily studies the wreck of his car.

Tegan is still recovering from the trauma of her possession by the Mara, and wants to return to Earth to rest in familiar surroundings. Instead, the TARDIS drifts into a warp ellipse and nearly collides with a spaceship travelling through the ellipse -- a fixed orbit through time and space. The Doctor is able to materialise on board the ship, which appears to be an opulent but deserted passenger liner. Exploring further, he and his companions find a transmat bay with an empty space where the capsule should be. According to the controls, someone left the ship six years ago... and went to Earth.

Brendon's Headmaster discusses the situation with Lethbridge-Stewart, and is reluctant to take any severe disciplinary action against Turlough -- an orphan whose affairs are dealt with by a very strange solicitor in London. Turlough is recovering in the school hospital, where he finds a crystal cube in his jacket; when he touches the cube it begins to glow and he is able to communicate with his new alien partner. Ibbotson arrives, and Turlough assures him that he'll take all the blame -- though in fact he's already told the Headmaster that he only went along to keep Ibbotson out of trouble. Turlough leaves hospital without waiting to be dismissed, and Ibbotson follows him to the obelisk on the hill above the school. There, Turlough follows the instructions placed in his mind, and presses the base of a stone urn -- releasing a camouflage screen around a transmat capsule. Ibbotson watches in shock as Turlough enters the capsule, which promptly disappears. Ibbotson flees back to the school and babbles everything to Lethbridge-Stewart, who is frankly sceptical; after all, a solid object just can't dematerialise...

Turlough emerges from the transmat capsule aboard the alien ship, which he hopes to use to return home; but his new partner won't release him from his contract so easily. Before he can go home, he must fulfil his side of the bargain and kill the Doctor. Meanwhile, the Doctor, Tegan and Nyssa return to the TARDIS but find that they are unable to dematerialise again. The Doctor soon determines that the transmat capsule has returned -- and that a signal being sent to it from a control box on Earth is interfering with the TARDIS. He returns to check the transmat controls and confirms that the capsule has just arrived from Earth, 1983. But what has it been doing there for the past six years?

The transmat control box short-circuits and explodes, blowing Turlough off his feet before he can strike. As soon as the beam cuts out, the TARDIS travels to Earth -- but vanishes before the Doctor and Turlough's eyes. At that moment Lethbridge-Stewart arrives to take Turlough back to the school, and although the Doctor is delighted to see his old friend, the former Brigadier doesn't recognize him at all. The Doctor soon realizes why -- or so he thinks -- but although he explains that he's regenerated since they last met, this means nothing to Lethbridge-Stewart, and the Doctor realizes that he has no memory whatsoever of their time together. When the Doctor tries to jog his memory by mentioning UNIT, Lethbridge-Stewart agrees to speak with him privately in his cottage, to find out what this strange young man knows about that top secret organisation.

Tegan and Nyssa emerge from the TARDIS by the obelisk, and as the Doctor isn't there to greet them Tegan worries that the transmat capsule may have malfunctioned. As she and Nyssa gaze at the school below, the capsule materialise nearby, and they enter -- to find the hideously burnt body of a man, about the Doctor's height and general shape. They assume that something has gone terribly wrong with the transmat process, and drag the barely conscious man -- whom they assume to be the Doctor -- into the TARDIS to recover. Tegan decides to seek help from the building at the base of the hill, while Nyssa stays with the Doctor; before leaving, Tegan takes a homing device so she can find her way back to the TARDIS easily.

The Doctor learns that Benton has retired and now sells used cars, while Harry Sullivan has been seconded to NATO. But when he inquires after Jo Grant, Sarah Jane and Liz Shaw, Lethbridge-Stewart begins to feel oddly uneasy -- and when the Doctor mentions Yeti, this opens a floodgate of old memories, of Cybermen, Axons, Daleks, Zygons... and the Doctor, in all his past incarnations. Lethbridge-Stewart wonders how he could ever have forgotten, but when the Doctor suggests he might wish to seek treatment Lethbridge-Stewart loses his temper; he eventually calms down and admits that some years ago, after retiring from UNIT and taking on his teaching position here, he suffered a nervous breakdown, apparently brought on by overwork. The Doctor is pleased to have met his old friend again but soon must get back to the business at hand -- locating his TARDIS, Nyssa, and Tegan. Lethbridge-Stewart recalls once meeting an Australian girl named Tegan... and the Doctor realizes that his TARDIS has materialised in the wrong time zone. And hidden within his old friend's fractured memories are the clues he needs to find it again.

Tegan reaches the school and meets a younger Lethbridge-Stewart, who tries to help her find "Turlough"'s listing in the school register. He is unable to locate any such student, but when Tegan mentions getting help back to the TARDIS, he instantly realizes who her injured friend must be. He sends a student to fetch Dr Runciman and accompanies Tegan back to the TARDIS, but as they go, she sees that the school is preparing to celebrate the Queen's Silver Jubilee. Since the Doctor was expecting to arrive in 1983, but the TARDIS has materialised in 1977, perhaps the man from the transmat capsule isn't really the Doctor after all...

Turlough decides to skip out of his contract and escape from Earth in the transmat capsule -- but the Black Guardian appears in his dreams in the form of the Headmaster, tricking him into revealing his intentions, and Turlough realizes that he'll never be freed of his bargain. Waking in a panic, Turlough wraps up his control cube in his bedding and climbs out of the window. When the Doctor learns of his disappearance he realizes what Turlough intends to do. He's already worried about the high level of coincidence in this affair, which suggests that some cosmic influence is at work behind the scenes; but before he can deal with such abstract concerns he must deal with the matter at hand. And that means Lethbridge-Stewart must remember what happened to him six years ago, and who Nyssa and Tegan really pulled out of the transmat capsule...

The Doctor tries to get Lethbridge-Stewart to remember the events of 1977; not only is this the only way he can find his friends, but he suspects that the events are the cause of Lethbridge-Stewart's nervous breakdown. But at that moment he discovers the control cube wrapped up in Turlough's bedding, and after a moment's thought rushes off to the transmat capsule to stop Turlough from stealing it. Fortunately, Turlough had forgotten that the transmitter was broken. The Doctor returns Turlough's control cube without mentioning what it might be for, and repairs the transmitter, intending to reflect a signal off the ship, through the warp ellipse and back to Tegan and Nyssa in 1977. As he does so he suddenly realizes the danger involved -- if the young Lethbridge-Stewart is to encounter the older Lethbridge-Stewart, the time differential will short out as per the Blinovitch Limitation Effect, releasing a catastrophic charge of temporal energy. As Lethbridge-Stewart tries to remember whether he entered the TARDIS in 1977, Turlough slips away and secretly sabotages the transmitter, which explodes -- separating the Doctor from the TARDIS for good.

Tegan, Nyssa and the Brigadier are highly suspicious of the alien figure in the TARDIS, but Mawdryn claims that he is their friend the Doctor and that the unstable transmat induced a mutation during his regeneration. His condition seems to be deteriorating again and he insists that they take him back to the ship, where he may find a laboratory which can help. Tegan is particularly suspicious, especially when the communications console begins to beep and then abruptly stops; but as they have no absolute proof to the contrary, they must give "the Doctor" the benefit of the doubt. Nyssa programmes the TARDIS to reverse its last journey and materialise aboard the ship, and the Brigadier accompanies them. There, Mawdryn departs, telling them to remain where they are as the presence of other life forms may inhibit his regeneration. The Brigadier gives him a moment to get clear and then follows him, just in case, while Tegan and Nyssa remain in the TARDIS. But the Brigadier loses Mawdryn in the ship's corridors and soon becomes lost.

The elder Lethbridge-Stewart clearly recalls the TARDIS departing without him -- and, to the Doctor's delight, he also recalls Tegan giving him the homing device as they approached the TARDIS. The Doctor fetches the homing device from Lethbridge-Stewart's cottage, repairs it, and determines that the TARDIS is now back on board the alien ship. Obviously the alien did not trust the transmat to return him safely and somehow convinced Nyssa and Tegan to take him back. The Doctor takes the homing device back to the transmat capsule; he can use this to home in on the TARDIS, transmatting safely back to the ship. Lethbridge-Stewart and Turlough both insist upon accompanying him. Once aboard the ship, they find a room which the Doctor hadn't encountered last time, and the Doctor sends Turlough to find the TARDIS, while he and the Brigadier investigate. Beyond the mysterious door is a laboratory containing a metamorphic symbiosis generator. This is Gallifreyan technology, used by Time Lords in regeneration crises -- and it's been stolen from Gallifrey and modified.

Mawdryn's condition continues to deteriorate until he is forced to crawl along the corridors of the ship, his skin blistering and running. By the time he reaches his destination he is too weak to open the secret panel, and must abandon his fellows and crawl further onwards to the laboratory. Turlough happens along moments later, trying to contact the Black Guardian for further instructions. The Guardian orders him to open the panel, which he does -- releasing the creatures beyond, seven other aliens of Mawdryn's kind. As Turlough flees in terror, the aliens stir to life; surprised that Mawdryn is not there, they set off in search of him.

The Doctor studies the modifications to the regenerator, commenting that they could do very nasty things to a Time Lord. Lethbridge-Stewart hears a noise in the corridor outside, sets off to investigate, and just misses running into his younger self. He returns to the laboratory to find a charred and pustulent body lying on the floor, and assumes that it's the Doctor. But when he helps the man into a regenerator cubicle and operates the controls at its instructions, the damage to the creature's body is repaired -- and it proves to be Mawdryn. Lethbridge-Stewart threatens to cut off the power if Mawdryn doesn't explain himself, but that doesn't faze Mawdryn. The Brigadier can't kill him... because he cannot die.

The Doctor returns to the TARDIS and finds Nyssa and Tegan, and is appalled to learn that they brought the younger Brigadier with them. He rushes back to the laboratory with them, and moments later, Turlough arrives. But the Black Guardian won't let him take off -- he must remain on the ship to witness the Doctor's final defeat.

Time Lords can only regenerate twelve times, and the Doctor has already used up four of his. If he gives his regenerative powers to the mutants, allowing them to die, he will never be able to regenerate again. They have experimented for centuries and have been unable to find a cure for their condition, but the Doctor refuses to give up his eight remaining lives to get them out of the mess they've made for themselves. The Doctor and his companions depart, and the mutants allow them to go peacefully -- for Mawdryn knows that the Doctor will return, of his own free will...

The Black Guardian discovers that the two Brigadiers are present on the ship, and orders Turlough to ensure they do not meet. Turlough emerges from the TARDIS and locates the younger Brigadier, and offers to take him to the Doctor. In fact, Turlough tricks him and locks him in the chamber from which the mutants earlier emerged. Turlough then returns to the TARDIS just as the others arrive, and the Doctor tells him to find the younger Brigadier and take him to the transmat. The homing device will allow the transmat capsule to transfer into the TARDIS once the TARDIS is clear of the ship. Turlough returns to fetch the younger Brigadier -- but, much to the Black Guardian's fury, the Brigadier has already escaped.

Mawdryn and the other mutants watch as the TARDIS dematerialises -- and the younger Brigadier then arrives. Realizing the danger, Mawdryn ushers the Brigadier off to the transmat capsule so he can return to Earth. But the Doctor and his companions have run into a problem; Tegan and Nyssa have collapsed on the floor of the TARDIS, their skin disintegrating just like Mawdryn's. The aliens' past experimentation to find a cure has resulted in a viral side-effect, and Nyssa and Tegan were infected when they carried Mawdryn from the transmat capsule to the TARDIS. The Doctor is able to reverse the effect by travelling back to the ship, but when he tries to negotiate the warp ellipse in the opposite direction Nyssa and Tegan revert to childhood. Once again the Doctor must return to the ship to reverse the effect -- and as the TARDIS is unable to leave the ship, the transmat capsule is unable to dematerialise as well. The younger Brigadier emerges from the capsule to find himself still on board the ship, and sets off in search of the Doctor.

The Doctor emerges from the TARDIS to confront Mawdryn, who admits that Nyssa and Tegan have been infected, although not deliberately. The aliens have found no cure for the degeneration, and they will fall subject to it whenever they travel through Time -- and as they must negotiate the warp ellipse to leave the ship, that means they will be trapped here for the rest of their lives. Their only hope is to share in the Doctor's life force, and the mutants refuse to allow them to use the laboratory unless the Doctor allows them to share in the power as well. The Doctor has no choice; in order to save his companions' lives, he must give up eight of his own. Lethbridge-Stewart accompanies them to the laboratory to operate the regenerator while the Doctor, Nyssa, Tegan and the mutants connect themselves to it. But as the regenerator begins to power up, the younger Brigadier hears the sound and approaches the laboratory to investigate. Turlough, warned by the Black Guardian of the danger, arrives moments too late. The younger Brigadier enters the laboratory just as the transfer is about to take place -- and the elder Brigadier finally remembers what happened to him six years ago. Before the Doctor can do anything, the two Brigadiers touch, and there is a colossal explosion...

In the corridors outside, Turlough is surprised to find that he is still alive... and when he takes the control cube from his pocket, he finds it cracked through.

The Brigadier's timing has been impeccable. The release of temporal energy was redirected through the regenerator at the moment of transfer, curing Nyssa and Tegan and killing the mutants while allowing the Doctor to retain his eight remaining regenerations. Mawdryn is the last to die, grateful that his journey is finally over. With the death of the mutants the ship begins to drop out of orbit, and as the Doctor and his companions carry the groggy Brigadiers back to the TARDIS, Tegan takes the opportunity to thank him for risking his lives for their sake.

While Nyssa waits in the TARDIS corridors with the recovering Lethbridge-Stewart, the Doctor and Tegan take the unconscious younger Brigadier back to 1977. There, as Dr Runciman arrives in response to his earlier request for help, the Brigadier stirs to life just in time to see the TARDIS vanish without him. The Doctor then transports the elder Lethbridge-Stewart back to 1983, where he announces that he's feeling better than he has for six years. The Doctor then remembers about Turlough and enters the TARDIS to rescue him from the aliens' ship, only to find that Turlough has already stowed away aboard the TARDIS. Turlough asks the Doctor for permission to join his company... and Nyssa and Tegan share a doubtful glance as the Doctor happily welcomes him aboard.