On Gallifrey, someone on the high council is perpetrating a treasonous act - transmitting the Doctor's bio-extract from the space/time matrix to an anti-matter being. On Earth, two English lads spend their last night in Amsterdam sleeping in a crypt where they're attacked by an alien creature under the same anti-matter being's control.
With an anti-matter being trying to enter the universe through the Doctor, risking the destruction of everything, there is only one clear course of action for the High Council of Time Lords to take: execute the Doctor. Meanwhile, Tegan arrives in Amsterdam and hear about what's become of her cousin from his unscathed friend.
Something seemed amiss about the Doctor's execution, so the Castellan has Commander Maxil discreetly but fully look it. Meanwhile, as the Doctor meets the anti-matter being inside the Time Lord Matrix, Tegan and her cousin's friend run afoul of a bird-like alien back on Earth.
The Doctor talks to Ambril and Chela to try and stop the 500th anniversary celebrations. A possessed Tegan finds herself in Dugdale's Hall of Mirrors to where she summons Lon. The Doctor and Nyssa return to the caves.
With the TARDIS trapped on a collision course with a strange, orbiting spaceship, locked in time as well as space, the Black Guardian recruits a deceitful and ill-natured British student to kill the Doctor.
The TARDIS lands on Earth six years out of date, stranding the Doctor in 1983 while leaving Tegan and Nyssa to look for him in 1977, eventually to discover a badly injured man that may very well be the Doctor. Both parties also encounter former Doctor-companion Brigadier Lethbridge-Stewart, though in 1983 he curiously has no memory of the Doctor at all.
Danger and discovery await the Doctor back aboard the alien ship, where a modified piece of Time Lord technology awaits his discovery. The Black Guardian is pleased with the Doctor's return and uses Turlough to awaken the ship's undead inhabitants to lead the Doctor to his death. The one uniting factor for all is the unforeseen presence of two Brigadier Lethbridge-Stewarts aboard ship, which could put a sudden end to everyone's plans if they're not kept apart.
Mawdryn and his fellow immortals - stuck in ceaseless cycles of mutation and deterioration - are quite determined on the Doctor sacrificing his future for their sakes, giving him the choice between helping them or stranding Teagan and Nyssa with them on their infinite journey. The Doctor, however, seeks a third option.
Under the directives of the Black Guardian, sabotage by Turlough destabilizes the TARDIS, causing it to latch onto the nearest spaceship for physical support. Nyssa, trapped inside her dissolving room, crosses onto the other ship in order to survive, entering onto an eerily automated ship marked with painted skull decals just as it's being invading by raiders.
The Doctor's party remains divided and scattered as the immense transport docks at the Terminus space station, which turns out to be a leper colony at the exact center of the known universe. As they find their way around and investigate, Nyssa shows signs of contracting the disease.
Since the Doctor's party represents neither lazars nor handlers, they're presumed to be investigators, which is enough to spark the disgruntled Valgard into challenging Eirak over leadership of the handlers. Meanwhile, as the giant, dog-like Garm takes a terrified Nyssa off for "treatment," Bor returns from the forbidden zone with interesting news about the ship.
In attempting to reopen a doorway into the TARDIS, Turlough activates Terminus' automated fuel-jettisoning sequence. The first time this sequence was engaged, it flung its first of two massive loads of unstable fuel into the distant past, producing the Big Bang that created the universe. This second sequence - if the Doctor can't find a way to shut it down - will release a second massive load, the explosion of which will entirely negate the effects of the first.
Captain Striker and his officers reveal themselves to be Eternals, mind-reading creatures who live outside of time and who require Ephemerals (humans and other "time dwellers") to relieve them of their emptiness. They race against other Eternals for the grand prize of Enlightenment, by which to grant their deepest wishes. That can't be good for the universe, but how can the Doctor strategize against beings adept at reading his every thought?
Turlough's panic puts him aboard a pirate ship where Captain Wrack uses his presence to invite all the other captains over for dinner. She's been picking off a few of her greatest rivals in the race and now sees an opportunity to clear the field once and for all and become the clear winner.
Tegan isn't aware she been outfitted with a devise to destroy Captain Striker's ship. While the detonation will merely slip the indestructible Eternals back into the realm of eternity, nothing nearly so elegant or as tidy awaits the Ephemerals aboard the ship.
In 1215 at the castle of Ranulf Fitzwilliam, son Hugh is jousting on a matter of honor against Sir Gillis Estram, the champion of King John, when the TARDIS appears. The Doctor, Turlough and Tegan are immediately hailed as demons and welcomed warmly by the King. Something is wrong with this picture, observes the Doctor.