Plot

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The Storyline of Doctor Who: Legacy starts in the tutorial and develops throughout the seasons of the game, mainly through cutscenes in the levels. It's main plot involves an army of time-travelling Sontarans changing history to create the ultimate war. An army of Zygons is also introduced in Season 6, and in the end the Master is revealed as the new enemy, concluding in a cliffhanger which will be developed in Season 5.

Tutorial

The Tutorial is where the storyline begins. 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 and create the ultimate war. After recruiting Jenny Flint, he decides to go back in his own timeline to get allies from his past to defeat the Sontarans and fix time.

Season 7

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

Season 6

This season begins with a prologue, a battle against a Sontaran military vessel near Androzani Major. In this season, the Doctor recruits his Third Incarnation and discovers that the Sontaran has recruited the Zygons to help them, among other enemies from season six. The Zygons then impersonated several of his allies and is revealed that the Zygons tried to ambush the Sontaran, but failed, and the surviving five were captured and offered to join forces to survive.The Sontaran threat continued concluding with a two-wave fight against the Sontaran Captain Vade the Defiant.

The Doctors and their allies enter a time storm centered around a man-made paradox on the day of December 25th and after overloading the paradox, they find Captain Jack Harkness. When they close the paradox down, he explains that the Sontarans and the Zygons were stopped by a new threat which was ripping time apart, destroying civilizations and causing the Fall of Sontar. This threat was revealed to be the Master and his Toclafanes. He has tracked down the coordinates of his old friends to help the Doctors to defeat the Master.

Season 5

The Doctor and his friends enter the Christmas Time Storm, where they battle enemies from their Christmases past. They see a Sontaran squad be obliterated by a single Toclafane, but they manage to defeat the Toclafane before it reports their location to the Master. They then continue to move forward into the time storm battling old Christmas foes, near the end a paradox opens inside the TARDIS bringing several wooden cybermen through as well. When it's closed the Doctors' war incarnation comes through. The storm paradox in which the cybermen came through takes them to Christmas on Trenzalore, but they manage to escape after the storm dies. After fighting winders, smilers and Solomon's robots again, Jack gives them the coordinates to find Ianto.

After searching for him in 21st Century Cardiff, they fall into several bubble universes throughout their journey. They 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. After that they're pulled back through time to Krop Tor and then fight against all the enemies of season six and seven before confronting the original Master and some Toclafane. Lastly, they encounter another time splinter before defeating a massive Zygon paradox and recruiting the Ninth Doctor and begin to plan a way to take down the master, and find out the only way is to take the Toclafane down...