The Doctor, Martha, and Jack materialise in a London alleyway, having used Jack's Vortex Manipulator, repaired by the Doctor, to escape the Futurekind in the year 100 trillion. Seeing "Vote Saxon" posters everywhere, and Saxon himself on a giant TV screen, the Doctor and Martha realise that the new Prime Minister, the mysterious "Mr Saxon", is the Master.

In 10 Downing Street, the Master speaks briefly with Tish Jones, who is unsure of her duties in her new job there. Next he enters the newly rebuilt cabinet room. After calling the cabinet members traitors, because they abandoned their parties to join his electoral bandwagon, he puts on a gas mask and activates jets of poisonous gas. As the cabinet collapses, the Master beats his hand on the table, drumming out a four-beat rhythm.

Journalist Vivien Rook obtains an interview with Master's wife, Lucy Saxon, as a pretext to warn Lucy that "Saxon" did not exist eighteen months ago — his entire life before that is a fabrication. Mrs Saxon turns to the Master, who is now standing by the door. He confirms that Saxon doesn't exist, and then introduces his "friends", four floating, metallic spheres, which materialise and kill Vivien. The Master promises his wife that "everything will end tomorrow".

Meanwhile, the Doctor, Martha and Jack have gone to Martha's flat to find out more about the Master's "Saxon" persona. Part of his apparently varied history is the Archangel network, a mobile phone network which Saxon was in charge of launching. The Master then makes a televised announcement about the Toclafane, the spheres seen earlier, saying that first contact will take place the following morning. The Doctor is surprised; the name Toclafane is that of a Gallifreyan fairytale villain, not a real alien race. As the Master makes his speech, the Doctor discovers a bomb on the back of Martha's TV. They make it outside just as her flat explodes.

Martha rings up her mum to check on her; Francine asks Martha to come to her house, claiming that she plans to get back together with Clive. She passes the phone to Clive, who tries to warn Martha away; however, the "sinister woman" is listening and orders police to arrest the entire Jones family. Martha hurriedly drives to the scene with the Doctor and Jack. On the way she phones Tish in Downing Street, just as Tish is dragged away by guards. Martha arrives at Francine's house, but the police open fire on her car and she is forced to drive away.

As the Doctor, Jack, and Martha abandon the car, Martha phones Leo to warn him, and is relieved to learn that he is in Brighton. Saxon interrupts the conversation and the Doctor takes the phone. He tells the Master about the Time War and how it ended. The Master reveals that he was resurrected by the Time Lords in order to fight in the war, but ran away in fear. He then informs the Doctor that they are now Britain's most wanted terrorists and tells them to run, noting that Jack's friends have been sent on a wild-goose chase in the Himalayas.

One of the Toclafane appears before the Master, asking if the "machine" is ready. The Master confirms it will reach critical mass at 8:02 AM, two minutes after first contact. The Toclafane warns of an impending "terrible darkness" and suggests that they flee, but the Master merely reminds it of its deadline.

As they hide in an abandoned building, the Doctor gives Martha and Jack some insight into the Master's background, explaining that Time Lords on Gallifrey stare into the time vortex at the age of eight: some are inspired, some run away, and some are driven mad. The Doctor ran and never stopped, but he believes the latter happened to the Master. After Jack receives a posthumous message from Vivien Rook to Torchwood about the Archangel network, the Doctor discovers that the Master is transmitting a mysterious four-beat rhythm that subliminally persuaded people to vote for him, which also kept the Doctor from previously detecting the Master. The Doctor then adds a perception filter to the TARDIS keys, allowing the trio to move about unnoticed.

While the TARDIS crew look on, US President Arthur Winters arrives in Air Force One. He tells the Master that UNIT now controls the operation. Citing a 1968 United Nations protocol, Winters insists on moving first contact to the neutral ground of the UNIT aircraft carrier Valiant and conducting the meeting himself. The Master brings Martha's family along, and the Doctor and friends follow using Jack's Vortex Manipulator. Onboard the Valiant, they find the TARDIS, its cloister bell ringing and the interior glowing an ominous red. It has been "cannibalised" by the Master into a paradox machine, set to go off at 8:02 AM. The trio head for the room where first contact is being made. The Doctor has a plan: if he can get his TARDIS key around the Master's neck, everyone will see him for what he really is.

When first contact begins, the Toclafane complain that the President is not the Master. The Master reveals himself and has his friends kill the President. The Doctor is captured by guards, and the Master temporarily "kills" Jack with his laser screwdriver, which is also equipped with LazLabs genetic manipulation technology. Coupled with biological data from the Doctor's severed hand, stolen in the previous episode, it allows the Master to artificially age the Doctor by 100 years. The Master brings in Martha's family to witness his triumph.

With the paradox machine ready, the Master tells the people of Earth that it's "the end of the world" and plays "Voodoo Child". The machine activates, creating a massive rift above the Valiant from which six billion Toclafane emerge. He orders them to kill one tenth of the Earth's population. He refuses to reveal the Toclafane's true identity to the aged Doctor, saying that the revelation would break the Doctor's hearts. Whilst the Master is distracted, Martha glances mournfully at the Doctor, Jack, and her family, then teleports to Earth using the Manipulator, promising to return as she watches the Toclafane descend. The Master and his wife look down on "his new dominion", with the aged Doctor between them, forced to confront his failure to stop the Master.