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.
The Doctor and Peri arrive on Karfel, a planet ruled by fear where the enemies of its ruler, the despotic Borad, are banished into a time tunnel known as the Timelash.
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?
In the year 2035, convict James Cole reluctantly volunteers to be sent back in time to discover the origin of a deadly virus that wiped out nearly all of the earth's population and forced the survivors into underground communities. But when Cole is mistakenly sent to 1990 instead of 1996, he's arrested and locked up in a mental hospital. There he meets psychiatrist Dr. Kathryn Railly and the son of a famous virus expert who may hold the key to the Army of the 12 Monkeys; thought to be responsible for unleashing the killer disease.
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The Doctor and his companions arrive on a spaceship headed for Earth, populated by natives of Earth from various different eras and commanded by the leaders of the Urbankan race. What are the Urbankans' intentions when they reach Earth?
The TARDIS lands on the idyllic jungle world of Deva Loka, which is being surveyed for possible Earth colonisation. Deva Loka is already home to a race of apparent savages, however: a mysterious people with strange powers which have mentally unbalanced the members of the expedition. To make matters worse, an ancient enemy of the natives known as the Mara is intent upon revenge, and latches onto Tegan's mind as its bridgehead to victory.
An Edwardian yacht in deep space races around the planets. There is a double agent in the TARDIS crew. The White Guardian warns the Fifth Doctor of great danger. Turlough must finally choose sides and at the end of the race lies the prize of Enlightenment.
The Fifth Doctor, Tegan and Turlough arrive on Sea Base 4, a nuclear warhead station under the sea that has some very nasty neighbours.
While investigating a vanishing Concorde at Heathrow Airport, the Doctor and his companions are thrown millions of years back in time, when a mysterious alien called Kalid is trying to control the ancient powers of the Xeraphin.
Omega, an ancient Time Lord made of pure anti-matter, once defeated by the Doctor, is plotting to cross over into this dimension by bonding with the Doctor. Meanwhile, the disappearance of a man in Amsterdam piques the curiosity of his cousin, Tegan, who previously left the Doctor at Heathrow Airport and now finds herself at Omega's mercy. Fearing total destruction from the collision of matter and antimatter, the Time Lords recall the Doctor to Gallifrey to undertake the only viable solution: executing him!
Tegan falls once more under the influence of the Mara and directs the TARDIS to the planet Manussa. There, the Federator's son Lon and his mother Tanha are preparing for a ceremony to celebrate the banishment of the Mara five hundred years earlier. The Mara takes control of Lon and uses him and Tegan to obtain from Ambril, the Director of Historical Research, the 'Great Crystal' - the large blue stone that originally brought it into being by focusing energy from the minds of the planet's one-time inhabitants. The Mara now plans to use the crystal during the ceremony to bring about its return to corporeal existence.