The Doctor and C in MI6
Intelligence agents around the world are being killed, resulting in The Doctor and her three travelling companions, Graham O'Brien, Ryan Sinclair and Yasmin Khan, being called in by the head of MI6, a person called ‘C’, to investigate, as the intelligence agent deaths it seems were not caused by humans.
Their only lead is a Daniel Barton, the CEO of a search engine media company, VOR. Additionally, The Doctor contacts Agent O, an agent who was tasked with monitoring extra-terrestrial activities, before being struck off by C. However, before they can learn anymore C is killed by mysterious lifeforms, but The Doctor, Graham, Ryan and Yasmin manage to escape unhurt.
While Ryan and Yasmin investigate Daniel Barton (whose DNA, they discover, is only 93% human) he extends an invitation to them to attend his birthday party the following day. Meanwhile The Doctor and Graham travel to the Australian outback to locate Agent O. Both groups, in their separate investigations, encounter the same lifeforms, who appear to be working with Daniel Barton.
The Doctor, with the help of O, is able to capture one of the lifeforms. However, unbeknown to her while sneaking into VOR headquarters with Ryan, Yasmin is captured by one of the alien lifeforms. She finds herself in a strange environment. Somehow, the captured alien is able to free itself by replacing itself with Yasmin and leaving her in The Doctor's cage at Agent O's base. Ryan, not knowing what has happened to Yasmin, is brought to Australia and regroups with The Doctor, Graham and, to his relief, Yasmin.
Joined by O, the four investigate Daniel Barton at his birthday party. The Doctor confronts Daniel Barton, who denies all of The Doctor’s accusations. Angered, Daniel Barton leaves in his car. The Doctor and her companions give chase on motorbikes finding themselves at an airfield where they discover Daniel Barton has a private jet. Leaping aboard the jet as it takes off, The Doctor becomes suspicious of O, who then reveals he is actually The Master - having been in control of Daniel Barton and the aliens the whole time.
Daniel Barton disappears from the pilot seat, leaving a bomb in his place. As the device detonates, The Master escapes while The Doctor is captured by one of the aliens and finds herself in the same environment Yasmin was in earlier, leaving Graham, Ryan and Yasmin in the falling plane.
To her surprise, in the aliens' dimension, The Doctor meets computer pioneer Ada Lovelace and grabs her hand when one of the aliens appears, transporting them to an invention exhibition in 1834, where they encounter The Master. Though The Master reveals that he knows the aliens are called Kasaavins, The Doctor realises that The Master does not fully understand them when he asks her how she managed to escape from their dimension.
Escaping from The Master, who uses his Tissue Compression Eliminator on some of the guests, Ada Lovelace takes The Doctor to the residence of polymath Charles Babbage. There The Doctor summons a Kasaavin, via a figurine identical to the one in Daniel Barton's office, hoping that the alien will return her to the 21st century. However, Ada Lovelace grabs The Doctor's hand as she fades away and they accidentally travel to Paris during World War II. There they are rescued by British spy Noor Inayat Khan, though The Master continues to pursue them through the use of a perception filter posing as a Nazi officer. The Doctor arranges to meet The Master atop the Eiffel Tower, where The Master reveals that he had the Kasaavins kill the spies to get The Doctor's attention. He also claims, to The Doctors disbelief, that Gallifrey has been destroyed.
With help from Ada Lovelace and Noor Inayat Khan, The Doctor destroys The Master’s perception filter and turns the Nazis onto him, while her group uses The Master’s TARDIS to return to the present. Meanwhile, Ryan finds instructions to safely land the plane with help from a recording left by The Doctor. However, Daniel Barton has branded Graham, Ryan and Yasmin as persons of interest and so find themselves on the run. After nearly being caught they manage to steal one of Daniel Barton's cars, which leads them to a warehouse containing another figurine.
Speaking at a conference, Daniel Barton reveals that the Kasaavins will rewrite humanity's DNA to utilize its storage capacity as hard drives. The Master, forced to live through the 20th century without his TARDIS, arrives in time to see the figurine device activate, only for it to fail after it is revealed that The Doctor had planted a virus in it so exposing The Master's treachery. The Kasaavins are forced back to their dimension, though they take The Master with them while Daniel Barton escapes.
With The Master’s plans thwarted, and before they leave in the TARDIS, The Doctor sets up the means for Graham, Ryan and Yasmin to survive the plane crash and to return Ada Lovelace and Noor Inayat Khan to their respective time periods – at the same time wiping herself from their memories. She then discovers in the TARDIS a recording, left by The Master for her, where he confesses to destroying their home planet after realising their understanding of Time Lord history was a lie. He also mentions ‘The Timeless Child’. The Doctor visits Gallifrey to discover it in ruins - confirming The Master's claim.
Afterwards, when reunited with Graham, Ryan and Yasmin, her travelling companions request The Doctor explain to them who she is, so she tells them of what she believes to be her backstory.