It’s one year since the Master has taken control of the planet. Martha Jones arrives in England on the coast, coming by boast, and meets with Thomas, a member of the UK underground. She has already made arrangements to meet with Professor Docherty, and the two of them take off.
Aboard the flying Valiant
aircraft carrier, the Master once more shows the aged Doctor the Earth under his dominion, and boasts of his plan to use the Toclafane to create a new Time Lord Empire. He’s well aware of what Martha is up to and demands to know what the Doctor told her a year ago before she teleported away. The Doctor refuses to tell him anything and the Master orders his staff to prepare for “launch” in 24 hours.
Jack is imprisoned aboard the Valiant
while the Jones family act as servants fro the Master. They stage a breakout attempt but the Master is well-aware of their plans and stops them, having Jack gunned down. The Doctor tries to use the Master’s laser screwdriver against him, but the isomorphic controls only respond to the Master’s touch.
Martha and Thomas get to Docherty just as the Doctor broadcasts a speech of his newest victory. he dismisses the claims that Martha is some kind of legend, and uses his laser screwdriver to age the Doctor 900 years while keeping him from regenerating. The Doctor is reduced to a shriveled dwarf-like figure and the Master exults in his victory. Martha is simply inspired, realizing that the Doctor is still alive.
Docherty, a scientist, has determined that the Master’s Archangel satellite system is still broadcasting subliminal messages keeping the people of Earth from rising up against him. Martha is interested in the Toclafane, and reveals that the only one that was defeated was hit by a lightning bolt. She has the readouts from the incident and gives them to Docherty. The professor figures out the exact electrical voltage and the three of them set a trap capturing one of the spheres.
The Master and his “wife” Lucy go to the now-imprisoned Doctor and talk of how they have seen the future… the future of Utopia, where humanity explored but found nothing. At the same time, Martha and the others open the Toclafane sphere and find… a human head. It has the memories of all of the Utopia settlers, and reveals that they found nothing where Utopia was rumored to be. They cannibalized themselves, regressing their minds to a childlike state. The Master found them and brought them back in time to serve as his army, with their willing help. To do so, the Master has converted the TARDIS into a Paradox Machine to avoid the paradox of the Toclafane destroying their own ancestors. The Toclafane are happy to help, thinking it’ll be fun.
Martha then explains that she has the weapon they need: a weapon crafted by UNIT and Torchwood capable of killing a Time Lord despite his regenerative abilities. It requires four chemicals, and she has spent the last year acquiring three of them. The fourth is at an abandoned UNIT base in London, and she and Tom set off to recover it. They take refuge for the night in a resistance shelter where Martha tells tales of the Doctor, nothing that it isn’t her story that is important.
They’re interrupted when the Master arrives: Professor Docherty gave him Martha’s location in return for her son’s safety. Martha surrenders herself and the Master destroys her weapon. He threatens to kill her as well but Thomas races out and the Master ruthlessly shoots him down. He insists that he’ll take her up to the Valiant
so the Doctor can witness her death personally.
Aboard the Valiant
, the Master takes the vortex manipulator Martha used to escape him previously and prepares for the launch of the fleet of spaceships he’s had built. The aged Doctor, Martha, Jack, and the Jones family are forced to look on as the countdown to launch begins at two minutes. Martha starts to laugh and reveal that everything is going according to plan: her plan and the Doctor’s. The weapon was a ruse, and the real purpose for her year of traveling was to spread stories of the Doctor, so that everyone would think of him at one key moment: 15 seconds before launch. The Master’s own telepathic Archangel system will pick up the telepathic impulse… which the Doctor has had a year aboard Valiant
to attune to. At 15 seconds, everyone on Earth thinks of one word: “Doctor.” The resulting telepathic energy fills the Doctor, giving him the power to restore his body to normal. The Master is powerless before him and the Doctor utters the three words his archenemy can’t stand: “I forgive you.”
The Toclafane realize something is wrong and attack the Valiant
, and a desperate Master uses the vortex manipulator to teleport himself and the Doctor to the largest shipyard on Earth. The Master threatens to activate the black hole drives of every ship, destroying Earth, but the Doctor calls his bluff, pointing out the Master would never kill himself. The Master reluctantly turns over his controller and they teleport back to the Valiant
Jack leads an assault against the Toclafane, fighting his way to the TARDIS. Only his immortality gets him through and once inside, he destroys the Paradox Machines. The timelines reset as the Toclafane never came to Earth, and only those aboard the Valiant
are immune as Earth rewinds itself one year in time. No one else has any memory of the Master’s reign of terror.
The Doctor prepares to imprison the Master in the TARDIS, but Lucy Saxon grabs a gun and shoots down her “husband” for betraying her. The Master refuses to regenerate, preferring death over eternal imprisonment. As he dies in the weeping Doctor’s arms, he wonders if the drumbeats in his head will finally stop.
The Doctor disposes of his rival’s body by cremation, in a brief private ceremony. However, as he leaves a feminine hand reaches into the ashes and takes out the Master’s ring.
Later in Cardiff, Jack prepares to say goodbye to the Doctor and Martha. He wants to stay on Earth to help rebuild Torchwood and deal with alien menaces when the Doctor isn’t there. The Doctor warns him that there’s nothing he can do about Jack’s immortality, although he may age as time goes by. As Jack leaves, he mentions that in his youth he had the nickname “The Face of Boe,” and they wonder if Jack will become their ally in the distant future…
Later, with the TARDIS repaired, the Doctor watches as Martha talks with her family at their flat. She comes into the TARDIS but announces that she plans on staying behind to earn her doctorate and take care of her family. She talks on unrequited love, although the Doctor doesn’t seem to know what she’s talking about. After she leaves, the Doctor prepares to depart… but something huge crashes through the wall of the control room. He determines that it’s the prow of an ocean liner… and picks up a life preserver with the words Titanic