The Doctor returns to Gallifrey, claims his rights and is inaugurated President. It soon turns out that he has led a group of aliens called Vardans to the planet to eradicate them completely. After they are destroyed, the Sontarans take their opportunity and follow them in their invasion until they are destroyed by the Doctor.

The Doctor, Jamie and Zoe return to Earth and become embroiled in the schemes of Tobias Vaughn. They meet up with an old friend, Colonel (now Brigadier) Lethbridge-Stewart, and some old enemies, the Cybermen.

The Third Doctor and Sarah arrive in 1970s London to find it has been evacuated because dinosaurs have appeared mysteriously. It turns out the dinosaurs are being brought to London via a time machine to further a plan to revert London to a pre-technological level.

The Doctor and Sarah return to Earth in the present day to find a strangely deserted village and woods stalked by white-clad figures.

The Doctor finally faces his destiny as both his home planet and old foe reappears.

The Doctor returns to Gallifrey to become the President of the high council of time lords. But Leela finds the Doctor is acting out of character and she is proved correct, when it is revealed that the Doctor has betrayed his own people and is working for Invisible aliens known as the Vardans who have taken control of the citadel and The Doctor has banished members of the high council and Leela to the wasteland outside the Citadel. But the Doctor has his own agenda, he is planning to thwart the Vardans scheme and time-loop their planet. But what the Doctor doesn't know, is that the Vardans are working for the Sontarans who are the real masterminds and are preparing to invade Gallifrey.

When scientists start to go missing in the 20th century, the Doctor is called in by the Brigadier to investigate. His investigations lead him to deduce that they are being kidnapped through time and he sets off in pursuit, unknowingly kidnapping journalist Sarah Jane Smith in the process. Arriving in the middle ages, the Doctor and Sarah find themselves caught up in the machinations of the robber baron Irongron and his man from the stars. The alien, a Sontaran named Linx, is arming him with modern weapons in return for helping him repair his damaged ship, and it's up to the Doctor and Sarah to stop him from ruining the Earth's timeline.

In England, 1066, the Doctor confronts a mysterious Monk who is attempting to change history.

The Master, in the guise of Professor Thascalos, has constructed at the Newton Institute in Wootton a device known as TOMTIT - Transmission Of Matter Through Interstitial Time - to gain control over Kronos, a creature from outside time. The creature is summoned but proves to be uncontrollable.

When Osgood is kidnapped by a rogue gang of Zygons, the Doctor, Clara and Unit must scatter across the world in a bid to set her free.