The Doctor

In an unknown time period, a war is taking place on an alien planet, fought with a mixture of primitive and advanced technologies. While running across a muddy war zone, a young boy finds himself trapped in a field of 'handmines'. The Doctor then arrives and tries to save the boy, tossing him his sonic screwdriver so that they can communicate. However, when The Doctor asks the boy his name, he is shocked and horrified when the boy answers with the name Davros - so revealing that he will become the future creator of the Daleks.

Centuries later, a creature named Colony Sarff, an agent of Davros, visits several worlds in search of The Doctor. His message for The Doctor is that Davros is dying and that ‘Davros knows, Davros remembers’. He reports to an ailing Davros that The Doctor cannot be located. Davros, still in possession of The Doctor's screwdriver, advises Sarff to seek The Doctor's friends, as they will be able to locate him.

On present day Earth, Clara is summoned by UNIT, to help them contact The Doctor, when every plane that is currently airborne has frozen. While trying to determine what is causing this and why, UNIT receives a message on a channel specifically created for The Doctor, should he ever need to contact them. The message's sender turns out to be Missy (aka The Master), who arranges to meet with Clara in an open-air café. Missy confirms that she froze the planes because she also needs Clara's help in finding The Doctor, as she thinks that The Doctor believes he has only one more day to live, and so is concerned for him.

Clara

Clara and Missy, with the help of UNIT, manage to track The Doctor to Essex in the year 1138, where he has spent three weeks partying. The trio's reunion though is cut short when Colony Sarff appears, having followed the two women to The Doctor's location. He reveals himself to be not a single entity but rather a colony of vipers composed of one large snake and several smaller serpents, filling out a monk-style robe to appear humanoid. He threatens everyone in the arena, but The Doctor rebuffs him. Colony Sarff then relays Davros's message for The Doctor and presents The Doctor's screwdriver. Shame overwhelms The Doctor – it is revealed (in flashback) that he didn't save the boy Davros, but instead, had abandoned him – and he agrees to be taken prisoner. Clara and Missy, over The Doctor's objections, insist on coming along as fellow prisoners, and Colony Sarff agrees. In the meantime, Bors, The Doctor's medieval friend – in actuality, a Dalek puppet – procures The Doctor's TARDIS for the Daleks.

Sarff takes the three to what appears to be a space station. The Doctor is brought to Davros, who tells The Doctor that he remembers what he did to him. Meanwhile, in another part of the space station, Missy notices that the gravity doesn't feel artificial, as would be expected on a space station. She opens an air lock and the pair step out apparently into outer space, until Missy realises that they are actually standing on a planet. As the illusion of outer space vanishes a city in the middle of a wasteland is revealed. Missy reacts with horror and disbelief, while Clara is left confused. At the same time, The Doctor is shown the truth by Davros – they are on Skaro, the Daleks' home world.

Missy

Sighted by a Dalek, Clara and Missy are taken to see the Supreme Dalek, who has a large weapon aimed at the TARDIS. Missy attempts to reason with the Daleks - if they don't destroy the TARDIS, she can help them fly it, allowing them to conquer the universe. However, the Supreme Dalek demands Missy's total extermination, and she vanishes in the blast. Realising that the Daleks are about to do the same to Clara, The Doctor begs Davros to save her, but Davros claims that he cannot control the Daleks. Clara, shocked by the death of Missy, does not know if to run or stay still. Davros observes the Daleks' choice to wait for Clara to run. When she eventually does try to escape, the Daleks exterminate her, causing her to vanish. The Daleks then use a laser on the TARDIS which also vanishes leaving The Doctor alone and powerless. Davros reasons with The Doctor that this happened because The Doctor showed him compassion as a child, despite knowing his destiny. Back on the battlefield the young Davros pleads with The Doctor not to leave asking if The Doctor has come to save him. The Doctor explains he's come from the future and that he has come to save his friend in the only way he can. Brandishing a severed Dalek gunstick The Doctor glares towards the child, shouting in anger ‘Exterminate!’

Clara, after being seemingly killed by the Daleks, finds herself outside the Dalek city with Missy. Missy explains to Clara that they both managed to escape by using the energy fired from the Daleks' weapons to teleport themselves away via their vortex manipulators. Meanwhile, The Doctor, not believing that Clara has been killed, forces Davros out of his life-support wheelchair and uses it to confront the Supreme Dalek. Safe from Dalek firepower, due to the wheelchair's force-field, The Doctor attempts to force the Daleks to find and return Clara to him, but they insist that she's dead. Then, without any warning, Colony Sarff appears in snake form from Davros' chair and forces The Doctor into unconsciousness.

Back inside the Daleks' city, Missy and Clara enter a Dalek 'sewer' - a graveyard for decaying, insane, and undying Dalek mutants. Missy uses Clara to lure and destroy a Dalek for its casing. She then forces Clara into the telepathically controlled Dalek casing in order to trick their way back into the main city. Missy directs Clara to make various statements and finds that if Clara attempts to say her name, the Dalek system translates it to ‘I am a Dalek’, and other attempts by Clara to express herself are translated as ‘Exterminate’.

Colony Sarff

The Doctor wakes up back in the infirmary with Davros revealing that the life-support cables surrounding him are connected to every Dalek on Skaro, which also keeps him alive. He tries to tempt The Doctor into destroying every Dalek using the cables, but The Doctor refuses. The Doctor reveals he came to Davros, not out of shame, but out of compassion for his sickness. Davros then opens his natural eyes and seeks The Doctor’s help to fulfil his wish to see Skaro's sun rise one last time. The Doctor agrees and so rewires Davros’ life-support system. But in doing so he realises that not even every Dalek in the city is enough to keep Davros alive for much longer. He then releases a small amount of Time Lord regeneration power into the cables to restore some of Davros' health. However, he has fallen victim to Davros' real plan: The Doctor’s regeneration energy is instead transmitted into every Dalek on Skaro. This increases their power and begins creating hybrid creatures. After breaking back into the city and abandoning Clara, Missy appears and saves The Doctor from the life-support system, killing Colony Sarff in the process.

The Doctor then reveals to Davros that he knew all along about his plan and allowed it to take place, as he also realised that Davros had not foreseen the full consequences. In reaching every Dalek on the planet, the regeneration energy simultaneously revitalises the decaying Daleks in the sewers, who break through the city's surface and attack the functional Daleks in revenge.

Upon fleeing, The Doctor and Missy run into Clara, still inside the Dalek casing. Missy lies to The Doctor, telling him that Clara was murdered by the Dalek in front of him and insists that he kill the Dalek in retaliation. Realising that The Doctor is about to shoot her Clara attempts to tell The Doctor who she is, but the Dalek’s speech system still translates her words into ‘I am a Dalek’ instead of ‘I am Clara’. But, when the Dalek/Clara pleads for mercy, The Doctor becomes puzzled as Daleks should not have a concept of mercy. He directs the Dalek to open its casing, and Clara is released. The Doctor simply orders Missy to run - which she does when she realises that The Doctor is likely to kill her for misleading him about Clara being in the Dalek casing.

After summoning the TARDIS back to them - which had avoided destruction through its Hostile Action Dispersal System (HADS) - with his new 'sonic sunglasses', The Doctor and Clara watch from afar as the Dalek’s city is destroyed. The Doctor wonders again why the Dalek (which Clara was trapped inside) asked for mercy. He then realises what he has to do. Using the TARDIS, The Doctor returns to the young Davros stranded in the battlefield and shoots the 'handmines' surrounding him using a Dalek gun. When the boy asks him which side he's fighting for, The Doctor takes him away from the battlefield, declaring that it doesn't matter what side he's on, so long as there is always mercy.