In ancient Rome, bathhouse architect Lucius (Hiroshi Abe) becomes famous with designing the original "thermae" (bathhouse). He receives an order to build a thermae in the colosseum to help gladiators recover from their wounds, but faces difficulties. Thus, Lucius travels again to modern day Japan through the time slip. He meets Manami (Aya Ueto) again, who is now a reporter for a magazine which covers bathroom. With the help of the flat face Japanese tribe, Lucius again designs a new thermae. Meanwhile, Emperor Hadrian (Masachika Ichimura) wants to keep the peace with the thermae, but the Senate wants to extend the land by using force. Emperor Hadrian and the Senate now have a confrontation and Rome becomes divided.
On the planet Alzarius in the alternate universe of E-Space, the Doctor, Romana and K9 find survivors of a crashed starliner, strange creatures lurking in the marshes and a genetic riddle which stretches back centuries.
Still trapped in E-Space, the Doctor, Romana, Adric and K9 encounter a medieval civilisation dominated by the Three Who Rule, vampires who govern from their mighty castle.
The Doctor, Romana, Adric and K9 encounter the enslaved time-sensitive Tharils, who lead them to a white void occupied only by the ruins of an old building and a spaceship - a dimension that might be the key to escaping E-Space.
The Doctor and Adric learn from the wizened Keeper of Traken that a great evil has come to his planet in the form of a Melkur - a calcified statue. The Keeper of Traken is nearing the end of his reign and seeks the Doctor's help in preventing the evil from taking control of the bioelectronic source that is the keystone of the Traken Union's civilisation.
After an encounter with the Master, an airline stewardess named Tegan Jovanka becomes an unwitting stowaway aboard the TARDIS as it travels to the planet Logopolis. There, the Doctor discovers that the Master's interference with the Logopolitans' advanced mathematics has unleashed a wave of entropy which threatens to consume the entire universe.
An alien intelligence hitches a ride onboard the TARDIS to 15th century Italy, where a deranged astrologer attempts to harness its power.
Summoned back to Gallifrey, the Doctor is framed for the assassination of the Time Lord President. To prove his innocence, he must stand for election himself, uncover the traitor in the Time Lord High Council, fight a hooded killer in a nightmare cyberspace world of his enemy's devising and battle against an old foe now out to destroy the Time Lords: The Master.
The Doctor arrives on a planet where two tribes, the savage Sevateem and the technically brilliant Tesh, are at war. He meets Leela, an exile from the Sevateem, and discovers that the tribes' god of evil is apparently himself...
Charged with genocide by the treacherous Valeyard at his trial, the Doctor receives help from an unlikely source to turn the tide of the High Council's rulings in his favour and reveal the Valeyard as a wrongdoer: the Master. For the Valeyard's own crimes are so atrocious, even the Doctor's archenemy will help him to ensure that the villain won't see the light of day again. Cornered, the Valeyard flees to the Matrix, where he can be the Doctor's judge, jury and executioner...
As evidence for the defense at his ongoing trial, the Doctor presents an adventure from his future when he is travelling with a computer programmer named Mel. Answering a mysterious distress call from the space liner Hyperion III, they find that the passengers aboard include unscrupulous scientists, secret agents, saboteurs, thieves and a murderer. And lurking in the shadows are the Vervoids, the product of sinister botanical experiments, who will stop at nothing to destroy all non-plant life.
As the Doctor's trial continues, evidence is presented showing his most recent adventure, one where he faces an old adversary, Sil. As a scientist conducts his unethical experiments to prolong the life of Sil's boss Kiv, the Doctor's memories of the events begins to return and an unpleasant surprise awaits him.
The Doctor is summoned before the High Council of Time Lords to stand trial for the charges of harmful interference to the course of events during his travels which have threatened the sanctity of the universe. Indignant at these accusations, the Doctor pleads his case to the Inquisitor with the hope that she will see him as a source of hope and goodwill for existence. However, his prosecuting attorney, a sinister Time Lord known simply as the Valeyard, begins a crusade against the Doctor with the motive of framing him as a villainous renegade.
A race of giant Gastropods has taken over the planet Jaconda. Their leader, Mestor, now intends to cause an enormous explosion in order to spread his people's eggs throughout the galaxy, and he kidnaps juvenile twin geniuses from Earth to work out the necessary mathematical equations. Space fighters led by Lieutenant Hugo Lang are dispatched to get the twins back, but they come under attack and Lang is the sole survivor when his ship crashes on the asteroid Titan III. A newly regenerated Doctor and Peri become involved and help Jaconda's elderly former ruler Professor Edgeworth, who is really a Time Lord named Azmael, to defeat Mestor and free the planet's bird-like indigenous people from the gastropods' reign of terror. Azmael, however, sacrifices his life in the process.
At the Tranquil Repose mortuary, the Doctor and Peri uncover a sinister plot to create a new breed of Daleks under the supervision of the mysterious Great Healer.
Suddenly gripped by a memory of being executed in his second incarnation, the Sixth Doctor travels to Seville to save his past self and ensure his own existence in his present.
The Doctor discovers his old enemy the Master is intent on preventing Earth's industrial revolution in 19th century England. But the Rani, a second rogue Time Lord, has plans of her own...
An alien distress call draws the Doctor and Peri to Earth, 1985, where they uncover a Cyberman plot to change the course of history.
Captured in a time corridor, the Doctor and his companions are forced to land on 20th century Earth, diverted by the Doctor's oldest enemy - the Daleks. It is here the true purpose of the time corridor becomes apparent: after ninety years of imprisonment, Davros, the ruthless creator of the Daleks, is to be liberated to assist in the resurrection of his army. Not even the Daleks foresee the poisonous threat of their creator. Indeed, who would suspect Davros of wanting to destroy his own Daleks - and why? Only the Doctor knows the truth. Will he descend to Davros' level of evil to stop him?
The Doctor and Leela must catch a killer on a vast mining ship run by robots and humans.