The Doctor takes Donna on her first trip in the TARDIS, arriving in a shop what they believe to be Ancient Rome. As the Doctor shows Donna around, they're unaware that a red-robed member of the Sybilline Sisterhood is following them. However, when they see a large smoking mountain on the horizon, they realize that they're not in Rome, but in Pompeii… on day before the eruption of Vesuvius.
The Sister returns to the Sybilline temple and announces that the Blue Box has arrived as foretold in the prophecies. Meanwhile, realizing the eruption is imminent, the Doctor and Donna return to the shop only to find that the shopkeeper sold it to a local stoneworker, Caecilius. At Caecilius' house, the husband and his wife Metella are arguing with their lazy son Quintus. Their daughter, Evelina, has the gift of visions and is destined to join the Sisterhood. She inhales deeply of the fumes leading from a vent going into the mountain and sees a vision of a giant lava golem rising up through the heat.
As the Doctor looks for the TARDIS, Donna tries to get him to save the people but he warns that Vesuvius' eruption is a fixed point in time and there's nothing he can do to change history. A Sister continues to watch them and the Head Priestess warns that if the Doctor tries to defy the prophecy of chaos accompanying his arrival, they must kill him. She follows them to Caecilius' household where Donna insists that the Doctor and try and warn the family to escape. The Doctor refuses and makes small talk with the family while locating the TARDIS. He's preparing to leave when Lucius, Pompeii's Head Augur arrives to pick up the stone tablet he's commissioned based on his visions. The Doctor notices that it's inscribed with circuitry patterns. Evelina warns that her visions have shown the tablets are dangerous, but Lucius dismisses her concerns claiming female soothsayers are unreliable. Evelina and Lucius both speak of the Doctor and Donna, knowing their backgrounds and real identities in the future. Lucius speaks of "she who is coming" to the Doctor, while Evelina identifies him as a Lord of Time then collapses.
Donna accompanies Metella to Evelina's quarters where the ailing girl is put to bed. As Evelina lies down, Donna notices that her right arm is almost entirely petrified. Meanwhile, the Doctor is interested in the underground vent that releases the fumes from which Evelina gains her visions, and realizes all of the seers of Pompeii have similar vents. The vents opened after the recent shocks from Vesuvius and that's when the soothsayers suddenly became more accurate. However, none of them seem aware of the impending eruption.
The Doctor pays Quintus to take him to Lucius' household where they break in and discover that Lucius has commissioned more tablets, each from a different stonemason. Lucius catches them and has his guards hold them at spearpoint while speaking of creating a machine of the gods. Meanwhile, Donna tries to convince Evelina that there is a coming eruption. Evelina doesn't believe her and the Sisterhood sense through Evelina that Donna is spreading "false prophecy." The High Priestess, shrouded in her chamber, orders the Sisters to bring Donna to the temple so she can be killed as a false prophet.
The Doctor examines Lucius' stone tablets and realizes that together they make an energy converter. The Doctor acknowledges that Lucius has won and offers to shake his hand… then pulls it off at the shoulder. The arm, and most of Lucius' right side, are petrified. The Doctor knocks over the stone tables as a distraction using his sonic screwdriver then ducks out the window with Quintus. Lucius calls for the Lord of Pompeii to attack, shouting down into the vent in his household. The city starts to rumble with the sound of footsteps and as the Doctor and Quintus arrive at the Caecilius manor, a lava golem bursts through the volcanic vent. The Doctor tells Quintus and the servant to get buckets of water while he tries to communicate with it. However, it refuses to listen and the others throw water on it, draining away its heat and rendering it an immobile statue.
The Doctor notices that the Sisterhood has abducted Donna during the attack. He goes to the temple, knowing where it is from when he has met the original Sybil in the distant past. He frees Donna and the High Priestess reveals that she is almost entirely petrified, and the Sisterhood reveals that they are also partially transformed to stone. The Doctor realizes they've been infected and demands to know what alien is responsible. Finally the aliens speak through the High Priestess and identify themselves as the Pyroviles. They inform the Doctor they fell from the sky 17 years ago and are infecting human bodies so that they can reconstitute themselves. The host bodies have gained telepathic abilities because of sharing the alien consciousnesses, but the Doctor notes that precognition isn't a psychic ability, and wonders why they can't foresee the coming eruption. The Sisterhood attacks but the Doctor holds them off by bluffing with a water pistol, until they read his mind and realize it's harmless to them. The Doctor and Donna flee into the volcanic vents while the Pyrovile take full control of their hosts and have Lucius take the tables to the "Cave of the Gods" within Vesuvius, where the lava golems guard the entrance.
As they make their way into the volcano, the Doctor still refuses to help save anyone in Pompeii, much to Donna's disgust. They enter an enormous chamber deep within Vesuvius, where the lava golem minions are working under Lucius' direction. The Pyrovile, speaking through Lucius, inform the Doctor that their home world was destroyed and they now plan to conquer Earth, spreading sufficient fire to burn off the oceans. The Pyrovile-tainted debris, spread through the vents, has given the soothsayers their abilities.
The Doctor holds the lava golems off with his water pistol long enough for he and Donna to get into a small spherical ship with the tablets inside. Examining them, the Doctor realizes that they are converting the energy from the volcano to assist the Pyroviles. He can shut down the converted… but then Vesuvius will explode. It's his choice whether to allow the eruption and destroy Pompeii, or stop it and let the Pyrovile conquer the Earth. Donna, realizing what is at stake, finally support the Doctor's dedication to making sure history remains unaltered despite the many deaths in Pompeii, and together they deactivate the energy converter. As the lava golems start to burn through the hull, Vesuvius erupts as the Pompeii soothsayers glimpse their new future. The explosion destroys the Pyroviles and throws the ship, an escape vehicle, clear of the volcano where it lands outside Pompeii. As lava and ash sweep toward Pompeii, the Doctor and Donna get to Caecilius' home where the frightened family begs them for their lives. The Doctor ignores them and goes into the TARDIS with Donna, and as they dematerialize she demands that he save at least someone. He considers her for a few moments... then rematerializes and gets Caecilius and his family to safety.
Later, the group watches as Pompeii burns. Evelina no longer has her visions: Vesuvius' explosion opened a temporary time rift drifting into the past, granting the gift of prophecy. Now that they've moved temporally past the point of the explosion, she is free. Caecilius and his wife mourn and the Doctor asks that they not mention he was there. As the Doctor and Donna leave, he admits that she was right and that he does need someone to travel with him.
Six months later, Caecilius and his family have moved to Rome and start a successful business. Evelina is free of her visions and able to lead a normal life, while an inspired Quintus is training to be a doctor. The family also has a new shrine to the family's household gods: the Doctor and Donna.