Plot

The Storyline of Doctor Who: Legacy starts in the tutorial and develops throughout the seasons of the game, mainly through cutscenes. In Chapter 1, an army of time-travelling Sontarans is changing history to create the ultimate war. An army of Zygons is introduced in Chapter 2, and in the end the Master is revealed as the main enemy. Chapter 3 and Chapter 4 see the Doctor in all his incarnations continuing to battle the Master in all of theirs.

Tutorial

The Eleventh Doctor and Madame Vastra are in Cardiff, in 1978, when a Sontaran Invasion begins. The Doctor realises that the Sontarans are travelling back in time to change history. After recruiting Jenny Flint, he decides to go back in his own timeline and collect allies from his past to defeat the Sontarans and fix time.

Chapter 1 - The Sontaran Threat

After recruiting Porridge, Rory Williams and his own tenth incarnation, the Eleventh Doctor and his allies start fighting aliens and fixing time. They find Paradoxes, Reapers and other temporal distortions, including Sontaran armies disturbing fixed moments in time. Along the way, they bring in other companions and allies, including the sixth, seventh and eighth incarnations of the Doctor. The Season Finale involves a battle inside the Time Vortex against an army of enemies created by the Great Intelligence.

Chapter 2 - Enter... the Zygons!

The Doctor recruits his third incarnation and discovers that the Sontarans have teamed up with the Zygons. After trying and failing to ambush the Sontarans, the Zygons infiltrated Sontaran High Command and made a treaty between the two races, ensuring that the Sontarans will protect the Zygons from the changes in time. The Doctors ultimately face a battle against Sontaran Captain Vade the Defiant, who reveals there is a force that may be greater then the Sontarans.

The Doctors and their allies enter a time storm centered around a man-made paradox on the day of December 25. After overloading the paradox, they find Captain Jack Harkness, who explains that the Sontarans and the Zygons were stopped by a new threat. Time is being ripped apart, destroying civilizations and causing the Fall of Sontar. This threat is revealed to be the Master and his Toclafane.

Chapter 3 - The Rise of the Master

The Doctor and his friends enter the Christmas Time Storm, where they battle enemies from their Christmases past. They see a Sontaran squad obliterated by a single Toclafane, but they manage to defeat the Toclafane before it reports their location to the Master. They then continue moving forward into the time storm, battling a paradox inside the TARDIS that ultimately brings the War Doctor through. Jack gives them the coordinates to find Ianto.

After searching 21st Century Cardiff, they fall into several bubble universes and come across paradoxes created by the First and Second Doctors trying to get through the Time Storm. They meet the decaying Master for the first time on Alfava Metraxis, and later confront the original Master. After defeating a massive Zygon paradox and recruiting the Ninth Doctor, they begin plotting to bring down the Master and the Toclafane.

The TARDIS is damaged and forced to land. The Doctors decide they don't need an army, they just need to think like one, and so they begin to piece a machine together to punch through to Brigadier Lethbridge-Stewart. In the process, they get sucked into another bubble universe and attacked by the Masters. Once they reach the Brigadier, they are attacked by time sundered Whisper Men that are being pulled out of existence. They finally land in a paradox protected by Ogrons as the Fifth Doctor comes though.

Chapter 4 - Betrayal and Redemption

The Doctors discuss how to take the Toclafane down, realizing that the Library may hold the key. But a detour takes them to the future where they meet the Twelfth Doctor in Sherwood. A massive unstable paradox arises, and the Fourth Doctor falls though. The TARDIS finally lands in the Library, but all of the Doctor's incarnations vanish. Professor River Song appears and takes over as team leader, while the Doctor's allies search for a book that will help them disarm the Toclafane. After they confront Vashta Nerada and battle the Master, they are reunited with the Doctors.

Stopping to recruit a few more allies, the Doctors then split up to hunt for a crucial piece of Cyberman technology. The First Doctor travels to Antarctica, while the Twelfth Doctor confronts Cybermen and a Cyber King in London. Reunited once again, the team passes through a series of bubble universes and is sucked into a confrontation with Time Squids and The Crinis.