The Doctor, concerned about aspects of his adventure in San Francisco, checks out the Eye of Harmony to ensure all is well -- and triggers a trap set by the Master, which erases all memory of his identity. A voice in his head tells him to trust the TARDIS, and he allows his ship to transport him to I.M. Foreman’s junkyard, in the year 1997 AD. There, drug dealer Baz Bailey has cornered Sam Jones, a schoolgirl who informed on him out to the police, with the intention of forcing her to take crack and getting her addicted. The Doctor’s arrival interrupts him, and Sam flees as the police arrive. The Doctor attempts to confiscate Bailey’s stash of cocaine, but when the police arrive they arrest the Doctor for possession. Bailey, desperate to get his drugs back before his supplier demands payback, arranges for his supporters to cause a riot at the police station as a distraction; in the confusion, however, the Doctor manages to get away from his interrogators, and takes the cocaine with him to dispose of it elsewhere. Meanwhile, Sam is caught returning late to Coal Hill School by her teachers Vicky Latimer and Trev Selby, and in order to prove her story she takes them back to Foreman’s Yard -- where Bailey and his gang have just arrived in pursuit of the Doctor. The Doctor, still disoriented and unsure what’s going on, steps into the TARDIS and dematerializes, leaving Sam, Vicky and Trev at the mercy of the frightened, angry, and knife-wielding Baz.

The TARDIS takes the Doctor to a Paleolithic jungle, where an old man is arguing with three people who have stopped to help an injured caveman. The Doctor intervenes when the old man attempts to smash in the caveman’s head with a rock, and the moment they encounter each other, Time is suspended and the Doctor acquires the memories of the old man -- his first incarnation. Now understanding the First Doctor’s position, the Doctor nevertheless reminds him that he left Gallifrey because of the arrogance of his fellow Time Lords -- and if he kills this caveman for his own benefit, he will prove himself no better than they are. The Doctor departs, leaving the First Doctor with something to think about.

The TARDIS then materializes on a foggy hillside, where the Doctor meets a confused Roman legionnaire who can’t remember how long he’s been fighting, and who claims to have seen men with weapons that kill at a distance, and vehicles which move by themselves. Exploring further, the Doctor passes through a wall of mist and finds himself on a World War One battlefield, where he is captured by the equally confused German Lieutenant Lucke. Lucke, desperate to make sense of what’s happening, tries to shoot the Doctor, but at the last moment a general arrives and stops him. Realizing that the Doctor does not belong to this time zone, the general sends him via time machine to the HQ at the centre of the zones, but he arrives just as the human resistance overpowers the aliens who have brought them to this planet to fight war games. The Doctor meets his second incarnation, and once again Time is suspended while they share memories. This time the Doctor advises his past incarnation to summon the Time Lords for help, even though it will mean risking his own capture. The Second Doctor points out that by crossing his own timeline, the Eighth Doctor has risked changing history; there is no guarantee that the Second Doctor will survive his encounter with the Time Lords just because the Eighth exists. Nevertheless, he reluctantly agrees to do so, and the Eighth Doctor departs as the Time Lords arrive to put matters right again.

The Third Doctor, exiled to twentieth-century Earth, has just blown up a Sea-Devil base to save humanity, but in the confusion the Master has escaped from imprisonment. One abandoned hovercraft, a murdered motorist and a hypnotised policeman later, the Master arrives in Devil’s End to collect his TARDIS, but the Doctor and Jo are able to trail him there. They arrive to find him holding the white witch Olive Hawthorne hostage and awaiting his chance to kill the Doctor, but before he can do so Miss Hawthorne taps the power of the elementals in the crypt and the Master is overpowered by the sudden release of telekinetic energy. He escapes in his TARDIS, and the Doctor and Jo are forced to return empty-handed to UNIT HQ -- where they find the Eighth Doctor waiting. Once again the Doctors share memories, but the Third Doctor does so reluctantly, blaming the Eighth for the advice which resulted in his forced regeneration and exile. As the Eighth Doctor’s identity becomes more complete, he is beginning to remember things of his own accord, and he assures the Third Doctor that he will regain his freedom and end his third life with a noble gesture. The Master returns to make one final attempt to kill his enemy, but is caught off guard by the presence of a future Doctor, and the two incarnations join forces to drive him away again. The Third Doctor considers forcing the Eighth Doctor to give him his working TARDIS, but reconsiders and lets him go, returning to his exile of his own free will.

The TARDIS takes the Doctor to E-Space, where the Fourth Doctor and Romana have defeated the vampire Lords of a primitive planet; however, there remains the possibility that the vampire taint has not been fully extinguished. The Fourth Doctor discusses preventive measures with the rebel leader Kalmar, but while he does so Romana is led into a trap and captured by Lord Zarn, the leader of a vampire coven in the nearby forest. Zarn fears that the peasants, emboldened by the death of the Three Who Rule, will now turn on the other Lords, and intends therefore to transform the Doctor and Romana into vampires to create a new King and Queen. The Doctor goes to Romana’s rescue and manages to distract the vampires while she escapes, and the Eighth Doctor arrives just in time to save her from the pursuing vampires. He accompanies her back to Zarn’s mansion, where the vampires have all but drained the Fourth Doctor of blood; the Eighth sets a fire as a distraction, however, and enters to rescue his fourth self. The rebel peasants, realizing that the Doctor and Romana are missing, show up and make short work of Zarn and his vampires, and the Eighth Doctor saves the Fourth’s life by giving him a transfusion. The Eighth Doctor departs, with more pieces of his memory fitting into place.

Back on Gallifrey, the Time Lords detect temporal instability and discover that the Doctor is crossing his own timestream. An ambitious Time Lord named Ryoth, who has fallen afoul of the Doctor’s meddling in the past, urges that he be executed for the crime, but President Flavia chooses merely to keep him under observation. Ryoth, incensed, alerts the Celestial Intervention Agency, and the Interventionists decide to use him as a deniable agent. He is therefore taken to the legendary Timescoop, which was preserved after the Death Zone incident, and is left to use it as he sees fit. Ryoth locates the Fifth Doctor on the Eye of Orion and uses the Timescoop to send a Raston Warrior Robot after him. The Eighth Doctor arrives just in time, and the Raston robot, confused by the presence of two identical brain patterns in separate locations, is unable to decide which to attack first and seizes up. Ryoth, furious, transports a Sontaran patrol to deal with the Doctors, but they manage to convince Commander Vrag that the Raston Robot is a vital part of the TARDIS operating system. He thus reactivates it, and the robot slaughters its way through the Sontarans. The Doctors then rig up a device to generate temporal feedback, and when the infuriated Ryoth attempts to send a Drashig after them, it materializes instead in the Timescoop chamber, where it eats both Ryoth and the Timescoop machinery before being caught and destroyed by Chancellory guards.

The Doctor then arrives on a Gallifreyan space station, where the Sixth Doctor has just been found guilty of genocide and is being marched off to face execution. The time bubble as the two Doctors meet enables the Sixth Doctor to escape, but as they flee from the Station in the Eighth Doctor’s TARDIS, they realize that the trial is still going on; the “execution” was an alternate timeline forced into existence by the mysterious Valeyard. The Eighth Doctor’s arrival has put paid to that timeline, and the Sixth Doctor travelling with him is therefore a temporal paradox which will soon vanish. Before this can happen, the Doctors go to Gallifrey to contact President Niroc and demand an inquiry into the trial; why is it being held on a station so far away from Gallifrey and where did the Valeyard acquire the power to force an alternate timeline? As the flustered Niroc prepares for the inquiry, the Doctors contact former President Flavia, who was forced to step down following rumours that the Matrix had been compromised; the non-entity Niroc was unexpectedly elected in her place, and he has filled the High Council with his supporters and instituted new security procedures which have caused much unrest amongst the Shobogans.

With Flavia’s help, the Doctors ensure that Time Lords sympathetic to their cause will be on the board of inquiry into the trial. The anomalous Sixth Doctor finally vanishes after telling his story, but he’s lasted long enough for the Eighth Doctor to put the pieces together; the Matrix was indeed infiltrated by aliens working from a base on Earth, and the Celestial Intervention Agency deliberately devastated the Earth to protect their secrets. When the Sixth Doctor began to stumble across the truth, they struck a deal with Niroc and the Valeyard in order to get the Doctor out of the way and cover up their incompetence. The Master appears and informs the board that he has revealed the truth to the Gallifreyans, intending to provoke a rebellion and seize control of Gallifrey in the ensuing chaos. While Flavia tries to keep the angry Time Lords in check, the Doctor visits the Low Town where the ordinary Gallifreyans live, and convinces his friends amongst the Shobogans to hold off on the rebellion. It soon becomes clear that Flavia is unable to contain the political turmoil on her own, so the Doctor visits Rassilon’s Tomb and convinces the legendary Time Lord to release Borusa, who was a worthy politician before he fell victim to his own arrogance. Rassilon summons Borusa from an earlier timeline and sends him to the Panopticon, where the Time Lords, shocked by the return of the legendary figure, allow him to lead them to a peaceful solution. A deal is struck with the Shobogans, the corrupt High Council is impeached, and the Sixth Doctor -- having successfully defeated the Valeyard, his own dark side -- departs with his companion Mel.

The Doctor sets off for his final encounter with his seventh self. Seeking solace on the planet Metebelis 3, the depressed Seventh Doctor is captured by a giant spider who has survived the destruction of her colony, but the Eighth Doctor arrives and rescues him. When they meet, the Eighth Doctor’s memories are fully restored, and despite the danger to the timelines he warns his previous incarnation not to answer a call soon to be made by an old enemy. Nevertheless, the Seventh Doctor’s spirits have been restored, and he decides to face his fate knowingly. The Master, meanwhile, hoping to cheat death and lead the Doctor into a final trap, visits a tribe known as the Morgs and acquires one of their deathworms, symbiotic creatures which enable them to survive beyond death. Having absorbed the deathworm into himself, the Master then travels to Skaro to lay a final trap for the Doctor.