Another man is found dead, strangled by the Doctor's scarf, so the Doctor is put on trial. By some of the archaic rules of law, he's made to "prove" his innocence by becoming a test subject in a new tachyon experiment with time. The result will prove his innocence or guilt, so they say.
With the saboteur and murderer revealed and arrested, peace should now be restored, but a new threat emerges - a war-monger who's both ready and eager to aggress upon other worlds with a newly manufactured warrior army.
The Doctor, Romana and K-9 arrive on the forest planet Tygella, where the native Tygellans now live in a underground city, due to the carnivorous plants. Where the Doctor finds he has been wrongly accused of stealing the Dodechedron, the city's power source. Only to discover the culprit is Meglos, the cactus-like last survivor of the desert planet Zolfa-Thura and he bids to return the Dodechedron to Zolfa-Thura for his own evil purpose and plans to use it as a powerful weapon and he plans to wipe out Tigella.
With the TARDIS occupants trapped in a chronic histeratic loop (forever reliving the same moment in time), the devious Meglos - disguised as the Doctor - gains the trust of the Tigellans along with full and private access to their power chamber.
With the dodecahedron gone, the city goes power critical. Its death, imminent. With Romana seeking escape from Meglos' pirates, and Meglos seeking escape from the sealed-up city, and the Doctor himself seeking to understand what's been going on (and why everybody wants him arrested), religious factions move in to take over the city.
With the Doctor about to be ritualistically sacrificed to appease the god Ti for stealing the dodecahedron, Meglos and the pirates return to Zolfa-Thura with the dodecahedron to fire up an ancient weapon and blast Tigella out of existence.
In answer to a summons from the Time Lords, the Doctor heads the TARDIS for Gallifrey where he must return Romana, but having tasted adventure and seen foreign worlds, she's none too happy about the return. Their journey, however, is interrupted by a rare space/time phenomena that lands them - not on Gallifrey - but on Alzarius. There, humanoid inhabitants begin to encounter an infrequent but regular cycle of perilous weather, called Mistfall, that coincides with the emergence of dangerous creatures.
As the humanoid community takes refuge in their crashed spaceship, venomous marsh spiders begin to hatch from the local fruit while bestial marshmen emerge from the waters to walk the land. It is quite apparent that the marshmen desire entry into the spaceship. Meanwhile, as a curious marshchild shadows the Doctor, a group of teen rebels decides to take over the TARDIS.
Infection from a spider bite causes Romana's personality to change. Meanwhile the Doctor, after discovering that the spaceship society is in a perpetual state of repair and upgrade, has morality issues with the ship's leading scientist who readies himself to perform gruesome experiments on the live marshchild while it's fully conscious.
Marshmen invade the Terradonian ship thanks to Romana, who seems to be in communion with them. While the ship's inhabitants flee for their lives, the Doctor discovers a crucial fact why these humanoids can never return to the planet Terradon.
Looking for scientists to help them find a way out of E-Space, K-9 locates a habitable planet for them to check out. They find a tower harboring royals overlooking a single village of grubby peasants, no fauna other than bats, and a band of rebels hiding out from a severe law that prohibits learning.
The Doctor and Romana are escorted to the tower to meet the royal leaders, hoping they can find answers to why this society evolves backwards. The Doctor recognizes the tower as an old Earth spaceship, and further finds that the old fuel tanks, far from empty, are full - but with blood. Meanwhile, Councilor Aukon senses intelligence in Adric and selects him to be the their first "Chosen One."
The Doctor finds archive material in the TARDIS that tells him he's dealing with an ancient enemy of the Time Lords, a nearly indestructible king vampire who's ready to revive and reenter normal space, spreading death, once again, across the universe.
The Doctor joins the villagers' revolt against their vampire rulers, unsure how to kill the king vampire. Meanwhile Adric is first in line to join the new vampire order while Romana is laid out as a sacrificial Time Lord for the awakening king vampire and his swarm of bats.
While the Doctor and Romana desperately rack their brains over how to escape E-Space, Time Winds strike the TARDIS, damaging it and K-9. Strangest of all, it allows Biroc, a hurt and hunted lion-man, to enter, phased in time, and set the control coordinates at zero-zero, sending the TARDIS into a milk-white void. Before running off, he warns of others who will be soon following.
Three humorless men from a damaged bulk freighter find the TARDIS. Wearily, Romana returns with them to appraise the situation of their damaged ship but, because she's a time sensitive, winds up as a living navigational component to replace their time-sensitive Tharil (lion-man) who escaped. Meanwhile the Doctor, having found a gateway, is having a time with Gundans, robot soldiers programmed to kill.
While Biroc leads the Doctor to a view of the Tharil's lordly past, Romana learns more about the damaged freighter and the coldheartedness of its crew. Meanwhile Commander Rorvik, confounded by the time mirror inside the universal center gateway, ignores evidence that it's no simple mirror and decides to blast it, imperiling the lives of everyone.
The Doctor deduces that the freighter is a slave ship loaded up with Tharils to be sold as time machine components, but the immense weight of Rorvik's damaged ship, designed to contain the Tharils, is now collapsing the fragile void of the micro-universe in which they're all stuck, pulling everything inside ever closer.
Returning to N-Space, The Doctor and Adric are summoned to Traken, a planet of peace and harmony. The Keeper of Traken is nearing the end of his 1000-year-old reign and one of the Traken consuls is to become the next Keeper. The Doctor, Adric, Tremas (the Keeper Nominate) and Nyssa (his daughter) set about to stop the Melkur, a calcified figure believed to be a "Source of Evil" trying to destroy the Traken Union, only to later discover it is the guise of a old enemy of the Doctor - The Master - who plans to take control of The Source (the keystone of Union) so he can ...
Tremas claims counselor privilege to protect the Doctor and Adric from execution, though it binds his fate to theirs if they're found guilty of murder. Melkur strengthens his hold over Kassia while Seron decides to have rapport with The Keeper to learn truth, and Adric finds evidence of another TARDIS in the area.
With Tremas falling under suspicion, due to his association with the Doctor, a new Keeper Nominate is named. Now, with everything in place, Melkur has only a short wait before his full malevolence can unfold.
Preparing to overhaul his TARDIS, the Doctor goes to Earth to take fresh measurements of a police box. A figure in white observes, as the Master lies in wait with a puzzling predicament for his rival Time Lord.
With the threat of doom ever-present, the Doctor and Adric press on for Logopolis, where the muttered mathematical incantations of its people can completely overhaul the TARDIS. En route they discover an accidental yet demanding passenger on board while, all the while, the Master secretively journeys with them to ensnare the Doctor in a diabolical trap.
With Nyssa from Traken unexpectedly rejoining the group, Adric aids the Monitor of Logopolis in trying to save the Doctor before time runs out. The Master, at liberty to prepare, is finally ready to reveal his true target, which unknowingly sets off the biggest catastrophe of all time.
With the universe collapsing, the Doctor forms an uneasy alliance with the Master to save it. In case all does not go well, the Watcher takes the Doctor's companions to a safe place, but his plans for them don't stop there. The one hope for all lies back on Earth.