The Doctor and Her Travelling Companions

In the far future, the last of humanity is hiding from the last of the Cybermen, who have hunted them almost to extinction. As a pair of Cybershuttles arrive overhead, The Doctor and her three traveling companions (Graham O'Brien, Ryan Sinclair and Yasmin Khan) arrive and set up the means to protect the humans from a group of attacking Cyberdrones. However, their devices fail, and some of the humans are killed.

As the advancing Cybermen have cut them off from the TARDIS. The Doctor orders her companions to leave with the remaining humans on their spaceship, and get to safety, otherwise, since her companions are human, if they are caught they would be converted into Cybermen. But Ryan and another human named Ethan are separated by the Cybermen's partially cyberconverted leader, Ashad (The Lone Cyberman they encountered in the previous story, "The Haunting of Villa Diodati"). Ryan and Ethan eventually manage to escape by assisting The Doctor in hijacking one of the Cybershuttles, but the Cybermen pursue them in another Cybershuttle.

In deep space Graham, Yasmin and the other three humans Yedlarmi, Ravio and Bescot discover they are traveling through a battlefield surrounded by dead Cybermen. They board an abandoned Cybercarrier, which they believe can take them to Ko Sharmus, a haven which is supposedly home to The Boundary - a portal that can send humans to the other side of the universe where they cannot be reliably followed by the Cybermen. Graham and Ravio investigate and discover that the apparently abandoned Cybercarrier holds thousands of dormant Cyberwarriors just as Ashad and his crew dock their shuttle.

Ashad

Meanwhile, The Doctor, Ryan, and Ethan arrive on the planet where Ko Sharmus is. However, they discover that Ko Sharmus is a person who helped other humans through The Boundary but remained behind as a ferryman in case others had survived.

Back in space Ashad and his Cybermen begin drilling into the Cyberwarriors and starts to resurrect them, while Graham and Ravio return to the control deck. Ashad leads the warriors to the control deck as Yasmin manages to contact The Doctor, warning her that the Cybercarrier is almost there, but it is carrying thousands of Cyberwarriors.

Yasmin and Ravio

On the planet below Ko Sharmus shows The Doctor, Ryan, and Ethan The Boundary, which appears as a rippling sheet of energy. It unexpectedly clears, and The Doctor watches in horror, as on the other side of the portal the ruined capital city of Gallifrey is revealed. Then without warning The Master leaps through the portal and informs The Doctor that she should be afraid and that ‘everything is about to change forever’.

The Master persuades a reluctant Doctor to join him on Gallifrey, where he then forces her to enter The Matrix. There he shows her the secret history of Gallifrey and reveals that the Shobogans, not the Time Lords, were the original species on the planet. One of them named Tecteun, a space explorer, was the first to leave Gallifrey and spent an untold amount of time searching the stars where she eventually encounters an abandoned child. Taking pity on the child, Tecteun adopted her and discovered the child had the ability to regenerate. After studying The Timeless Child for many years (and forcing several regenerations to occur), Tecteun after grafting that capacity tests it on herself and successfully regenerates - so enabling the Shobogans, residing in the Citadel, to be transformed into Time Lords.

The Master then reveals that The Doctor is ‘The Timeless Child’ and that Tecteun and the child were inducted into a clandestine organisation called The Division - the details of which have been redacted from The Matrix. The Doctor's memories were subsequently erased, prior to the childhood she remembers.

Ko Sharmus

Leaving The Doctor trapped in The Matrix, The Master lures Ashad to Gallifrey and shrinks him with his Tissue Compression Eliminator, taking the Cyberium. With its knowledge, The Master creates a race of infinitely-regenerating Cybermen, using the bodies of the Time Lords, which he plans to use to take over the universe. Meanwhile in The Matrix, The Doctor sees a vision of one of her incarnations that she encountered in "Fugitive of the Judoon" - who gives her the means to escape by overloading The Matrix with all of her memories from her past regenerations.

On board the Cybercarrier, Bescot is killed, while Graham and Yasmin successfully hide from the invading Cybermen in empty Cyber-armour. They subsequently save the lives of Ryan, Ethan, and Ko Sharmus from the Cybermen forces sent to the planet by Ashad. The group gather and agree to go through the portal to Gallifrey. There they find The Doctor, who with the help of her companions, discover Ashad's miniaturised body. It is then that they learn about the ‘Death Particle’ which is capable of destroying all organic life on a planet. This particle is still inside Ashad’s miniaturised body and despite being miniaturised it is still deadly to all organic life. The Doctor and her friends blow up the Cybercarrier, destroying Ashad's army in the process and foiling his plot to rebuild the Cyber-Empire.

Finding unused TARDISes, The Doctor programs one to take her allies home. The Doctor then takes one of Ko Sharmus' explosives and attaches the miniaturised body of Ashad, still containing the Death Particle, to the explosive and sets off to confront The Master. However, when she encounters The Master and the Time Lord-Cybermen hybrids (whom The Master calls 'CyberMasters'), and despite being goaded by The Master to detonate it, she is unable to do so. But Ko Sharmus appears and takes the explosive, as penance for failing to suitably hide the Cyberium. The Doctor manages to escape in another TARDIS as the explosion consumes Gallifrey presumably destroying The Master along with the hybrids.

The Doctor's allies arrive on contemporary Earth in their TARDIS, while the TARDIS, that The Doctor borrowed, lands near her own and she enters it relieved that everything is in order. But as she prepares to take off, she is arrested by a Judoon and teleported to a prison located inside an asteroid.