Some six months after the events of "Mission to the Unknown", the TARDIS arrives on the planet Kembel, and the Doctor leaves the TARDIS to try and find medical aid for the wounded Steven, leaving him with the Trojan servant girl Katarina.
Meanwhile, two Space Agents, Bret Vyon and the injured Kert Gantry, are also on the planet trying to find out what happened to their agent, Marc Cory. Eventually Gantry tells Vyon to go on without him, as he will slow Vyon down. Seconds after Vyon leaves, a Dalek finds Gantry and kills him. Vyon then spots the Doctor leaving the TARDIS, and takes the key from him at gunpoint before knocking him out. Eventually finding the TARDIS, Vyon demands that the occupants take him off the planet, but Katarina barely understands what's going on, much less how to work the ship. Steven then briefly recovers and knocks Vyon out after seeing him threaten Katarina. The Doctor returns to the TARDIS and finds that Vyon left the key in the door. The Doctor freely enters the TARDIS and places knocked out Vyon in a restraining chair then goes back outside.
On Earth, Mavic Chen, Guardian of the Solar System, announces to the people that he will be going on a break. However, in reality he is joining the alliance that has been formed by the Daleks, and arrives on the planet Kembel soon afterwards.
Seeing Chen's spaceship (termed a "spar") arrive, the Doctor returns to the TARDIS, only to find it surrounded by Daleks.
Katarina had released Vyon, who cured Steven with some field medicine (two white tablets that he has in jacket pocket), and they meet up with the Doctor soon after, just as the Daleks set fire to the jungle in order to drive out any further intruders. While the alliance prepares for a meeting of its leaders, Chen and another leader, Zephon, watch the jungle burn. Chen goes to the meeting, but Zephon refuses to go with him, saying that he will go when he feels like it. The Doctor and his companions infiltrate the city, and spot Zephon going to the meeting. They knock Zephon out, tie him up, dress the Doctor up in Zephon's large cloak and send him to the meeting while the other three break into Chen's spar.
Arriving at the meeting, the other leaders express irritation at the lateness of "Zephon." The meeting begins, and the Dalek Supreme reports that their ultimate weapon, the Time Destructor, is now complete. Chen reveals that he has procured a sample of the extremely rare element taranium (it takes 50 Earth years to produce tiny amount of it), a vital part to operate the Time Destructor. Meanwhile, the real Zephon has managed to untie himself and sounds the alarm. In the resulting confusion, the Doctor steals the taranium and flees. However, Vyon hears the alarm and prepares to take off in the spar without him.
The Doctor manages to get to Chen's spar just in time for take-off. The Daleks blame Zephon for the situation, saying that his tardiness caused the Doctor and companions to find him, but Zephon defends his actions and accuses Chen of arranging to have the taranium stolen back. Chen says that Zephon's accusation is nonsensical and the Daleks agree, concluding that Zephon is the one who's responsible. Zephon tells the Daleks that two of the other leaders will also leave if he does, only to have the leaders in question to swear allegiance to the Daleks. Finally, Zephon announces that he is leaving the alliance. He does not get the chance — a Dalek kills him as he goes to leave.
On course for Earth, the Doctor reveals that he found a tape while he was in the jungle. The group plays it back, and it turns out to be from Agent Cory, whose brief statements confirm what they already know. As they near the prison planet Desperus — where convicts are simply left, without having any guards or means of escape — the Daleks use a randomiser to disable the controls of the spar. The spar crashes down towards the planet below, causing minor damage to the ship upon landing. Realising that the impact should have totally destroyed the spar, the four conclude that the Daleks want them alive and quickly begin repairing the ship. Upon seeing the landing, a group of prisoners attempts to get on-board, but the Doctor electrifies the ship entrance and the prisoners are knocked unconscious. A Dalek ship arrives, but misjudges it's landing and suffers a crippling crash. The spar manages to take off again, and Katarina goes to check the airlock but finds a convict who managed to get onboard just before take-off, the other prisoners having discharged the electricity in the ship's entrance.
The convict, Kirksen, holds Katarina at knifepoint and threatens to kill her unless the travellers take him to the nearest planet — Kembel. The group eventually decides to comply, but their decision soon proves irrelevant as Katarina activates the airlock, blowing her and Kirksen into space. Stunned, Steven suggests that she must have done it accidentally, but the Doctor thinks that it was deliberate.
Upon seeing the events, the Daleks remotely destroy the pursuit ship for their failure to land properly, but seem satisfied that the delay caused by the crash will allow Chen enough time to get to Earth and have the trio arrested when they arrive.
Arriving on Earth, the three evade detection, and go to see Vyon's old friend, Daxtar. Daxtar initially seems co-operative, but the Doctor realises he's allied with Chen when he mentions the taranium before anyone else does. Vyon quickly kills Daxtar, much to the Doctor's annoyance, but there's little time to dwell on this as Chen's security agents, led by Sara Kingdom, arrive. Vyon allows the Doctor and Steven to get away by throwing himself at Kingdom, but she overpowers and kills him. She orders Borkar, her colleague, to "shoot on sight" at the intruders.
Sara Kingdom chases the Doctor and Steven to a laboratory, where they are all accidentally caught up in a molecular dissemination experiment and are transported to the planet Mira.
Chen pretends that he planned this accident, and tells the Daleks where to find the Doctor and Steven. On Mira, Kingdom (who turns out to be Vyon's sister) is forced to join forces with the Doctor and Steven as they are attacked by savage invisible creatures. The Doctor and Steven manage to convince Sara of Chen and the Daleks' true intentions, just as a Dalek ship arrives. The Daleks fend off an attack from the invisible creatures, and demand that the three surrender. The Doctor reluctantly announces that "the Daleks have won."
Fortunately for the Doctor and his companions, more invisible creatures attack, allowing the three to escape and steal the Dalek ship. They try to return to Earth, but the Daleks take control of the ship remotely then use a magnetic beam to draw it to Kembel. Realising that they don't have much time, the Doctor decides to build a fake taranium core, which he can give to the Daleks while keeping the real one. Steven then gets the idea to charge up the fake core with gravitic energy, but in the process encloses himself in a forcefield and is left barely conscious.
Upon landing, the three negotiate with Chen (who has since returned to Kembel) to be allowed to conduct the handover of the (fake) taranium core at the TARDIS. The Daleks refuse, but Chen persuades the Daleks that they don't have anything to lose, thinking that the Doctor will be unable to stop them after the core has been handed over. The Doctor and Sara return to the TARDIS, while Steven hands over the core. The Daleks try to kill him, but the forcefield manages to protect him, though it is exhausted in the process.
After leaving Kembel, the TARDIS lands, but the Doctor warns that "the atmosphere outside is entirely poisonous."
The group has actually landed in 1960s England, outside a police station. They get themselves arrested, but later manage to escape. The TARDIS next lands on the set of a silent film, causing many problems for the film crew (such as the Doctor being mistaken for a cultural advisor and the lead actress nearly quitting because she thinks the director wants to replace her with Sara) before escaping. Upon their escape, they have a toast to Christmas, and the Doctor wishes a happy Christmas to the viewers.
Meanwhile, back on Kembel, the fake taranium core is fitted to the Time Destructor, which is then tested on another representative, Trantis, who has proven useless to the Daleks. However, there is no effect and the fake core quickly exhausts itself, leaving Trantis totally unharmed. The Daleks accuse Chen of lying about the taranium, when Chen realises that it was the Doctor that switched the cores. The Daleks send a request to Skaro for a time machine, in order to pursue the Doctor. Trantis is then killed by a Dalek.
The TARDIS briefly lands back on Earth during a cricket match, then on a volcanic planet. The three travelers have been followed by the Meddling Monk, who damages the TARDIS's door lock, then mockingly informs the Doctor and companions that they are stranded on the planet for the rest of their lives. Not to be deterred, the Doctor performs makeshift repairs to the lock, and gets back inside the TARDIS. The Monk is surprised by this, but follows the Doctor to his next destination.
Meanwhile, the Daleks' time machine has arrived on Kembel. The task force leaves in it and the rest of the Daleks join the Supreme in a victory chant.
The Doctor and his companions and the Monk arrive in ancient Egypt, along with Mavic Chen and the Daleks, who begin their search for the taranium.
Realising that the Monk and someone else has arrived, Steven and Sara go to find out who it is while the Doctor repairs the lock, but are arrested as looters by the guards of the nearby pyramid and accused of being in league with the Daleks, who have killed a number of other guards. While the two make their escape the Monk tries to find the Doctor, but is instead found by Chen who offers him an ultimatum — help them find the taranium or the Daleks will kill him. Unsurprisingly, the Monk accepts.
The Doctor sees the Monk and follows him back to the TARDIS, where he attacks him before leaving. Soon, Steven and Sara return, looking for the Doctor, but instead see a bandage-wrapped hand reaching out from a large box
It is the Monk, wrapped up by the Doctor. Steven and Sara take him to go and find the Doctor. However, they don't get far before being caught by the Daleks and Chen, who demands the taranium. In desperation, the Monk suggests using Steven and Sara as hostages. Chen accepts this, and tells the Daleks that the Doctor will not allow the two to be killed.
As the Doctor breaks into the Monk's TARDIS and steals something, Chen announces over a loudspeaker that unless he hands over the taranium, Sara and Steven will be killed. The Doctor is dismayed, but has little choice but to comply. When he hands over the core, the Daleks try to kill them and the Monk but they all escape, helped by an attack by the Egyptian guards. While the guards disable some of the Daleks, most of them escape and return to their time machine with Chen.
Back in the TARDIS, the Doctor admits that he did not have time to build another fake, and had to hand over the real taranium. But he's stolen the Monk's directional controller — evidenced when the Monk lands on an ice planet and realises that without having any control over the direction of his TARDIS he now has little chance of ever catching the Doctor.
The Doctor fits the control and takes off, but the console room is engulfed in a flash of white light.
The directional control has burnt itself out almost instantly (due to the Monk's TARDIS being a later model than the Doctor's), but it is enough to get them back to Kembel. The three leave the TARDIS, but Sara and Steven lose the Doctor in the jungle and proceed to the city alone. Upon arrival they find the Dalek city deserted, and the alliance leaders imprisoned. They agree to turn on the Daleks, and in exchange are released from the prison cell. They take off in their ships — apart from Chen, who is apparently killed when his spar explodes just after take-off.
Searching the jungle, they find the entrance to a second, underground city, which the Daleks are now using. As they prepare to enter, Chen returns, having faked his death, and takes the two prisoner. He leads them into the underground city.
They go through the underground city and Chen leads them into the control room in grandiose fashion. Thinking that he was still imprisoned in the first city, the Dalek leader announces that their alliance is over. Chen refuses to accept this, and proclaims himself the leader of the alliance. He tries to kill the Dalek leader, but his blast simply diffuses off the Dalek's shield. The Dalek orders Chen taken outside and killed, causing Chen to flee boasting that he is immortal. He's quickly proven wrong when a Dalek patrol corners him and guns him down.
Taking advantage of the distraction, the Doctor enters the control room and activates the Time Destructor. The Daleks return, but are powerless to do anything due to the danger of the Doctor increasing the Destructor's power. He orders Sara and Steven back to the TARDIS, but Sara refuses to go. The two flee with the Time Destructor through the jungle, which rapidly begins to deteriorate and die. The Daleks pursue them, but seem immune to the effects. The Doctor and Sara reach the TARDIS but have been aged massively by the Destructor. The two collapse and Sara disintegrates. Steven rushes outside and tries to deactivate the Destructor, but cannot do anything. As he begins to rapidly age, he tries to help the Doctor, but is ordered to get back into the TARDIS. Fortunately, when trying to deactivate the destructor he managed to reverse it, thus causing the two to revert to approximately their previous ages. The pursuing Daleks try to destroy the Destructor with their weapons but instead cause it to run uncontrollably fast, destroying the Daleks and reducing the planet to a lifeless, barely habitable wasteland.
The Doctor and Steven emerge from the TARDIS some time later, the Destructor having burnt itself out. "What a terrible waste..." mutters the Doctor, referring to the death and destruction that has taken place.