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.
This article may contain spoilers.
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.
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.
This season begins with a prologue, a battle against a Sontaran military vessel near Androzani Major. In this season, the Doctor discover an army of Zygons, among other new enemies. The Sontaran threat continues, concluding with a two-wave fight against the Sontaran Captain Vade the Defiant.
According to the game developers, the story will change dramatically in Season 5. The first levels will involve the team trapped in a time vortex around 25 December, as a long lost friend fights to get through them. There will be more interations and dialogues between the Doctors in the cutscenes. The War Doctor and Jack Harkness will be important characters in the season's plot. The Sontaran storyline will be wrapped up and a new major enemy will be introduced.