While on holiday in the Eye of Orion, the Doctor (Peter Davison) begins to experience flashes of pain, feeling as though bits of his existence are being removed from time.

In a garden somewhere on Earth, the first Doctor (Richard Hurndall) attempts to flee from a peculiar energy form which scoops him up and takes him away. Elsewhere, at a UNIT headquarters building, Brigadier Lethbridge-Stewart (Nicholas Courtney) is visiting with the new Brigadier, Charles Crichton (David Savile), when the second Doctor (Patrick Troughton) pays a social call, having seen a prestigious announcement in tomorrow's Times. However, the second Doctor and Lethbridge-Stewart encounter the same energy form which removes them from the world. The same effect also kidnaps the third Doctor (Jon Pertwee), driving alone on a British country road in his yellow roadster, Bessie, and Sarah Jane Smith (Elisabeth Sladen), having left her flat to catch a bus.

Somewhere, in a dark chamber, an unidentified man places figurines of each of his kidnappees on a playing field. He attempts to remove the fourth Doctor (Tom Baker) and Romana (Lalla Ward) as they are punting on the Thames river [using footage from the aborted story Shada], but a temporal eddy prevents this from happening, and the two are stuck in time. 

In the Gallifreyan capitol, President Borusa (Philip Latham) is unnerved as Chancellor Flavia (Dinah Sheridan) and the Castellan (Paul Jerricho) welcome the Master (Anthony Ainley) to a meeting. The Master, who is intrigued by their invitation, is startled to find that the Doctor's past selves are being taken out of time... and only he is ruthless and cunning enough to enter the Death Zone  Gallifrey's darkest secret  to rescue them. In return, the High Council promises the Master a new cycle of regenerations. Startled by the proposal, he accepts, and is transmatted into the Death Zone. 

The fifth Doctor sets the coordinates of the TARDIS, leaving a horrified Tegan (Janet Fielding) and Turlough (Mark Strickson) to their own devisings. Meanwhile, wandering alone in a twisting maze, the first Doctor encounters his granddaughter, Susan (Carole Ann Ford)... and a Dalek! They narrowly escape, and discover that they're on Gallifrey. The fifth Doctor's TARDIS arrives in the Death Zone, where he, Tegan and Turlough meet with the first Doctor and Susan to attempt to determine where they are. 

The third Doctor finds Sarah Jane just as they are attacked by Cybermen, and soon also encounter the Master, whom they do not believe is attempting to help them. Foiled by his attempt at honesty, the Master instead decides to ally himself with the Cybermen. 

The second Doctor and the Brigadier attempt to enter the Dark Tower, the center of the Death Zone, through an underground passage. Long ago, the Time Lords transported offworlders to the Death Zone using a time scoop, where they made their captors engage in gladiatory and blood sports. Upon their enlightenment, the Time Lords stopped this horrific practice and forbade use of the timescoop. Now, the only point of interest in the Death Zone should be the tomb of Rassilon, the first and greatest of the Time Lords who gave them the secret of time travel... but someone is using the timescoop again, exemplified when the second Doctor and Brigadier are attacked by a Yeti. 

The first Doctor and Tegan attempt to enter the Dark Tower through the front entrance, followed closely by the Master and the Cybermen. They attempt to solve several logic puzzles on their way in. 

The third Doctor and Sarah also attempt to enter the Tower, though they must pass a Raston warrior robot first before using its gear to enter the tower from the top, using cabling to transport themselves across the chasm. 

Meanwhile, another contingent of Cybermen is attempting to destroy the TARDIS. While the fifth Doctor is transmatted to the Capitol, Turlough and Susan watch helpless, the TARDIS drained of energy, as the Cybermen set up a fusion bomb outside to take care of them. 

The first, second and third Doctors, the Brigadier, Sarah and Tegan are all reunited in the tomb of Rassilon inside the Dark Tower, where the Master pulls his weapon on them. The Brigadier lends a hand, knocking out the Master before he is able to cause harm. They then set to work on deciphering an obelisk upon which is written some strange symbols in Old Gallifreyan. 

In the Capitol, the fifth Doctor, who has tangled with Flavia and the Castellan and has been forbidden to leave, is hunting around the President's office when he stumbles upon a secret chamber, unlocked by a musical tune noted in a painting of Rassilon. Inside the chamber, the Doctor is horrified his old friend Borusa is behind everything. Borusa, fearing the end of his regenerative cycle, has stumbled upon the secret of Rassilon's immortality, and has used the timescoop to bring the Doctor's former selves together, all to enter the Dark Tower and solve Rassilon's final mystery. Using the Crown and Sash of Rassilon, Borusa commands the fifth Doctor to do his bidding. After the past Doctors lower the forcefield surrounding the Dark Tower, both the TARDIS, carrying Turlough and Susan, as well as Borusa and the fifth Doctor all arrive, where Borusa reveals himself to everyone. The Brigadier, Susan, Tegan, Turlough and Sarah are incapacitated by Borusa's power. 

Suddenly, a voice from the darkness beckons. Rassilon, the greatest Time Lord of all, is alive in his own tomb, an ethereal presence in the shadows. President Borusa demands immortality. Rassilon asks the Doctors if Borusa is worthy of this gift, and all say no, all except for the first Doctor, who inexplicably agrees that Borusa is indeed worthy. Borusa receives his gift immortality is granted as he is encased in stone in the sides of Rassilon's tomb, there to spend forever in isolation and despair. 

Rassilon asks the Doctors if they wish immortality too, and naturally, they turn down the offer. The Master vanishes, as Rassilon notes that his crimes will find their punishment elsewhere; Rassilon also frees the fourth Doctor and Romana from their time loop, before vanishing into the ether. The first Doctor is very pleased with himself; he suddenly realized the true meaning of the Old Gallifreyan phrase on the obelisk, To lose is to win, and he who wins shall lose. He takes Susan into the TARDIS, as does the second Doctor with the Brigadier and the third Doctor with Sarah  before it splits into four forms, the first three vanishing into their own times and journeys. 

Chancellor Flavia arrives with a contingent of Gallifreyan guards to find the fifth Doctor, Tegan and Turlough. Flavia notes that the Doctor has evaded his responsibilities for far too long, and with Borusa now being noted as unavailable, the Doctor must take his place as Lord President of Gallifrey (see The Deadly Assassin). The fifth Doctor, unhappy with the task, tells Flavia to return to the Capitol and that she is in charge until his return, before he takes Tegan and Turlough and flees to the TARDIS. Once again, he says, he's on the run from his own people in his TARDIS... because, after all, that's how it all started.

Synopsis from Doctor Who: The Fifth Doctor Handbook by David J. Howe, Mark Stammers and Stephen James Walker, reprinted with permission; further reproduction is not permitted. Available from Telos