The Doctor, Tegan and Turlough land inside an undersea secret military base in wartime Earth, 2084. The base is about to be attacked on two fronts. Enemy agents within work to neutralize the base while an assault team of aquatic Silurians prepare without for a surprise attack.
Just are the Doctor gains a tentative trust from the humans, a Silurian battle cruiser approaches. The Doctor warns Commander Vorsha to hold his fire and find out what they want, but is the level-headed commander one who'll listen?
With Silurians and Sea Devils attacking the air locks, the saboteurs use the distraction to launch plans for disabling vital functions of the base. With all the strife going on around him, and an electricity-generating myrka on the loose, the Doctor endeavors to bring a little sunshine into their unhappy undersea lives.
The Malus, an alien that's purely evil, needs the civil war re-enactments to become authentic so it can feed off the psychic energy of dying and embattled men and fully revive. Not if the Doctor can derail things, of course.
Following the destruction of the TARDIS, the only part of it left is the hat stand. So Turlough uses it as a weapon! Plantagenet gets swallowed by the earth, and Norna and Turlough discover the Tractators.
The Doctor tries to deal with the Tractator's cunning plan, despite Turlough's best intervention. They discover the splintered TARDIS in the tunnels beneath the planet's surface, but how will they put it together again?
A time corridor forces the Doctor to the London docklands on present-day Earth where a bomb squad watches over some strange, alien canisters. At the other end, a battle cruiser lunches an assault on a prison space station that holds just one prisoner - Davros, creator of the Daleks.
While Davros looks into solving a small problem offered up by the Movellans, the Daleks have not overlooked the Time Lords for all their years of interest and attention paid them, hoping to make of the Doctor and his companions emissaries of their appreciation, in order to thank them all to the fullest and permanently.
The Doctor and Turlough arrive on Lanzarote to investigate a signal. Turlough rescues American Student Peri Brown from nearly drowning and discovers she has in her possession a data core from Turlough's home planet Trion. The Doctor, Turlough and Peri follow the signal to the volcanic planet Sarn, where the natives worship a fire god known as Logar, and where the Doctor learns The Master has accidentally shrunk himself after testing a more lethal version of his tissue compression eliminator and has taken control of Kamelion, using him to find numismaton gas that will ...
On the volcanic planet Sarn, Turlough recognizes several Trion artifacts that point to Malkon (the Chosen One among the Sarn people) being his own brother. Meanwhile, Peri flees from Kamelion who has almost been entirely possessed by the Master.
Sarn prophesy foretells of an outsider who will come to aid the people. It's a role the Master is more than delighted to fill, which finally presents Timanov, the Sarn religious leader, the unbridled support he's sought in his campaign to cull the faithless from among his people. Turlough's secret past, however, is somehow intricately involved in all this, and the reluctance of its disclosure is enough to threaten all friendly ties with the Doctor.
While the Master, victim of his own attempt to improve his TCE weapon, seeks restoration through Sarn's numismaton gas, the truth of Turlough's past comes out at last, though to guarantee the safety of his brother and the Sarn people, Turlough must consider a great personal sacrifice.
The Doctor and Peri get involved with drug running after landing on the twin planet of Androzani Minor and getting arrested as gun runners and targeted for execution. Not before Peri stumbles into some highly toxic and lethal plant life.
Having been saved from execution by Sharez Jek and his androids, Jek takes a shine to Peri, and wants her with him forever. Salateen tells the Dr and Peri that they are dying from Spectrox toxemia, but there is an antidote.
Chellak and his men attack Jek's base. The Dr crash lands the ship, and must escape from his captors, find the antidote to Spectrox poisoning and save Peri. He does so, but at the cost of his own life.
The Doctor's moods are wide and in a jumble as he settles into his new regeneration. Elsewhere a set of genius twins are kidnapped, whose mathematical computations can manipulate features of the universe. They're immediately put to work by aliens for an as yet unknown end.
The Doctor takes Peri to Titan 3, a desolate hunk of rock in space where he hopes to find some solitude for awhile. Instead he finds the lone but unconscious survivor of a recent spaceship crash in sight of a mound-shaped complex where no formalized structure should exist.
The Doctor arrives on Jaconda, once lush and green, to find it completely devastated by giant gastropods. Old legends about the planet's half-human/half-slugs weren't just myths after all. With or without help from the Doctor and his unpredictable mood swings, Lt. Lang is up for rescuing the twins, who are finally informed of the grand purpose they've been brought to Jaconda to accomplish.
The Doctor and Edgeworth deduce that the real plan of Mestor, the gastropod ruler of Jaconda, will not only destroy Jaconda but lead to the devastation of other planets. Together they hope to thwart him despite his formidable ability at slipping into people's minds and controlling them.