While on vacation in the year 2003, Benny argues with Jason and storms off to the isolated Turkish village of Dogubayazit to cool down; however, he has anticipated her and arrives there first. Benny goes to the hotel bar to avoid him, where she meets the members of two expeditions seeking Noah's Ark. Due to recent border skirmishes between Iran and Iraq, no Turkish soldiers are willing to risk escorting the expeditions through the danger zone. Benny, stung by one of the expedition member's sarcastic remarks, shows off by using her unlimited credit card to hire a group of soldiers as an escort. Both expeditions thus set off, and while Benny and her cheerful young guide Dilaver accompany marine biologist Bill Raelsen to Mahser Dagi, Jason -- to show that he's just as good as her -- accompanies former NASA astronaut and moonshot veteran James Edward Allen to the more traditional resting place of Mount Ararat.

Benny and her expedition locate drogue stones on Mahser Dagi, evidence that the Ark may be located here, but Benny becomes suspicious when she realizes that the holes in the stones are pointing directly towards Mount Ararat. When she analyses the stones' molecular structure, she discovers that it is changing, as if the stones are trying to avoid detection. Before she can investigate further, she and her friends are shot by an Iraqi soldier who caught them filming their discovery and thought they'd captured him on film. Benny is only wounded, and manages to stab the soldier in the eye with a fellow archaeologist's paintbrush before she collapses from loss of blood. The rest of her expedition is captured by Iraqi soldiers led by Colonel Samran, and only Dilaver manages to escape, when he receives a savage beating from the Iraqi soldiers and is left for dead.

Allen's expedition settles in on Ararat, where they use a frequency generator to locate what appears to be the outline of an ancient boat. However, tension develops between their guides, two farmers who claim to have seen the Ark, and their military escort, who believe the farmers to be untrustworthy. When the leader of the escort is found dead, a fight breaks out between the soldiers and farmers, until the elderly archivist Candy DuFries manages to show them that the Major was killed by a weapon without serrated edges, not the knife held by the farmer accused of the killing. At that moment, Iranian soldiers led by Captain Imrud Tammuz arrive and shoot everyone holding a weapon, including Candy, who was still holding the knife. Tammuz then confiscates the data collected by the expedition and imprisons the survivors, promising to release them once he has what he's come for. Allen attempts to flee with the expedition's data, but Tammuz shoots him dead; Jason manages to catch a glimpse of the data as he hands it over to Tammuz, but doesn't understand its significance.

Tammuz allows his prisoners to build cairns for their dead, and Jason attempts to bribe their guard to let them escape. The guard takes Jason's credit card but refuses to let them go, and Jason loses his temper and knocks him to the ground, accidentally killing him and enabling Jason and his friends to escape. They flee to Mahser Dagi, where they find the injured Benny and share their stories. Realizing that they need help to escape, Benny forces Jason to use their time rings to summon the Doctor. While waiting for help to arrive, Benny analyses Allen's souvenir moonrock, which the dying Allen had given to Jason, and discovers that it is made of the same mineral as the "drogue stones" which her expedition found. Both the Iranian and Iraqi soldiers are searching the area with Geiger counters, which suggests that they have located a new source of uranium which could change the political stability of the region if one side gets hold of it. Before she can put the pieces of the puzzle together, however, Tammuz and his soldiers arrive in pursuit of their escaped prisoners and run straight into Colonel Samran and his own team.

The Doctor and Chris arrive in a rented helicopter, only to find Benny, Jason and their friends caught in the middle of a firefight. Jason manages to get to the helicopter, but Benny rushes back at the last minute to rescue Dilaver; however, Dilaver is already dead, and she is captured by Samran. As Samran's troops open fire on the helicopter, the Doctor and Chris are forced to flee. Benny is then questioned by Samran, who threatens to kill her fellow archaeologists one by one until she satisfactorily interprets the data he and his men have collected. She tries to explain that the drogue stones on Mahser Dagi are part of an alien transmat device with some connection to the Moon, and that they are capable of changing their molecular structure to avoid detection -- but by disguising themselves as uranium they have attracted the attention of the Iraqis and Iranians, who are now fighting for possession of what they believe to be uranium reserves. Samran doesn't believe her claims, and when soundings detect a perfect cube buried beneath the mountain he forces the archaeologists to unearth it, believing it to be a secret American military outpost. He is unable to break in, however, and when he receives word that Iranian reinforcements are on their way, he plants explosives around the cube and leaves his prisoners, including Tammuz, tied up to die in the explosion.

Tammuz manages to free himself and prepares to flee, and in order to save the others Benny has no choice but to tell him how to operate the transmat controls on the side of the cube. They are all instantaneously transported to the Moon, where the shock of suddenly arriving in an airless environment causes Benny and Tammuz to lose consciousness and kills everyone else. Benny and Tammuz are then rescued by members of a UNIT team sent to investigate an alien artefact detected on the Moon by Allen's NASA expedition, but Tammuz doesn't believe that he has been transported to the Moon, and concludes that he's stumbled across a secret American military base in his homeland. Determined to teach the Americans a lesson, he begins shooting them one by one until a terrified technician agrees to help him activate the base's target sequence. The chief scientist, Liz Shaw, tries to stop Tammuz from activating the base's controls, claiming that this is alien machinery which they may not be able to stop once activated -- but Tammuz is now beyond reason, and he activates the transmat. Liz and the virulent Agent Yellow are transported to the surface of the Earth, along with the only sample of the antidote which may be able to prevent a worldwide catastrophe...

Jason tries to force the Doctor and Chris to return for Benny, but the Doctor instead hypnotises him and has him reproduce Allen's files from memory. As the Doctor sets off in the TARDIS to investigate further, Chris hacks into the NASA database and retrieves the classified files on Allen's Moon mission. It appears that Allen's mission detected an irregularity in the Moon's orbit which can only be caused by a singularity orbiting within the Moon itself; an expedition has been sent to investigate further, but if their tampering exposes the singularity, the resulting X-ray blast could wipe out all life on the hemisphere of Earth facing the Moon at that time. Jason, however, is unable to deal with such abstract dangers while Benny's life is in danger, and he holds Chris at gunpoint and forces him to return to the danger zone to rescue Benny. There, however, they find only the dying Liz Shaw, whose flesh is dissolving away from her bones; unable to save herself, she gives them the antidote, and orders them to inject themselves and then kill her. Chris and Jason inject themselves with the antidote but Chris is unable to bring himself to shoot Liz in cold blood. At that point they are confronted and arrested by a UN Hazmat team sent to quarantine the area.

Chris and Jason are taken back to the Hazmat team's base, where they are decontaminated and their minds are scanned by Imorkal, an Earth Reptile who has been working with Liz and is helping the UN during the crisis which Tammuz has precipitated. Having determined their innocence, team leader Fielding explains to Jason and Chris that a terrorist on the Moon has transported an alien terraforming virus into the Earth's biosphere. Liz is dying in agony as the virus causes chemical transformations which are turning the water in her body into sulphuric acid, and other products of the process are releasing an unknown chemical agent which is causing further chemical changes within the surrounding landscape. Agent Yellow is turning the Earth into the image of another planet on which humans cannot survive, and Jason and Chris have taken the only antidote in existence. Liz is being kept alive in agony until Imorkal can read her mind and determine the formula for the antidote, but just as he succeeds the virus escapes containment and the entire complex begins to dissolve as people's bodies spontaneously begin generating toxic chemicals.

Imorkal escapes with Chris and Jason, but realizes that he is dying and tries to implant the formula for the antidote in Jason's mind. Despite his best efforts, however, Jason succumbs to the race memory malaise which affects humans upon meeting Silurians, and is unable to retain the formula. Chris is in shock, and has mentally regressed to the trauma of Roz's death. He and Jason return to Dogubayazit, where the Doctor has tried to rescue as many villagers as he can; the Doctor attempts to get them into the TARDIS as safely as possible, but Agent Yellow escapes containment and begins to affect the interior of the TARDIS. The Doctor materializes on the alien base on the Moon and sends the others out while he tries to repair the TARDIS interior. Tammuz is still on the loose, and the firefight between Tammuz and the Turkish soldiers triggers self-defense systems in the base which attempt to cleanse the biological infestation; fortunately, the Doctor realizes what's going on just in time, and emerges from the TARDIS with portable force fields for the survivors. Tammuz flees into the depths of the base and two soldiers set off in search of him.

The American government launches nuclear missiles at the base, believing that terrorists have seized control of it and precipitated the crisis in Turkey. Chris and Benny manage to contact them and explain what has happened, but the missile launch control complex succumbs to Agent Yellow and is destroyed before they can abort the missiles. Chris manages to deactivate the missiles from the moonbase by remote control, but by this time the governments of Earth, attempting to halt the spread of Agent Yellow, have begun bombing the affected areas of Earth -- and as Agent Yellow is resistant to radiation the explosions are only spreading the contamination further and faster. Within forty-eight hours the Earth will be destroyed. As the Doctor seeks a solution, Jason accidentally activates a holographic historical record within the base -- which refers to him by name, and thanks him for his assistance to the Cthalctose race. Benny realizes that somehow he is responsible for what's happening here, and after a furious argument with her, Jason steals her time ring and uses it and his own to travel back in time, hoping to talk the species which built the moonbase out of their genocidal plan.

Jason materializes on 16 Alpha Leonis One, six billion years in the past, where the Cthalctose are facing extinction from a black hole which has entered their solar system. Protected from the sulphuric acid seas by his personal force field, Jason manages to communicate with the Astronomer Royal, who is building an ark with which to save his world. Jason offers a spare force field generator to the Astronomer, hoping that he can study the technology and use it to come up with an alternate plan, but before he can explain further the excited Astronomer Royal places him in suspended animation in case his services are needed later and takes the new technology to his people. Jason, trapped in suspended animation for a thousand years, watches in despair as the Cthalctose argue over how to use this new technology and even fight wars, while the black hole draws ever closer. Eventually, one faction attempts to use the force fields to prevent any more material from falling into the black hole, but the force field generators become surrounded by an impenetrable shell of solar material and the Cthalctose are thus unable to reach them and conduct maintenance. With little time left, the Cthalctose use the force field generators to generate and trap two singularities which they can use to power the Astronomer Royal's ark on their moon. Shortly after the ark is completed, the generators around the original black hole fail, and the sudden consumption of the massive shell around the black hole generates a radiation surge which sterilises 16 Alpha Leonis One. Jason eventually wakes and uses the time rings to return home, aware that his attempt to save the situation has instead created it, resulting in the death of at least one world, and possibly two.

Benny blames Jason for his lack of forethought, but the Doctor understands that he was trying to help, and reveals that material from the Cthalctose biosphere is now caked on the outside of Jason's force field. The Doctor uses this to create an antidote to Agent Yellow, and after inoculating Benny and the villagers he uses the ark's transmat to send his "Agent Scarlet" to the infected areas of Earth. The fallout from the nuclear bombs, however, sterilises Scarlet before it can act, and as the villagers start to fall victim to Agent Yellow he realizes that his antidote was ineffective in any case. The Doctor now has no choice but to order Chris to reactivate the nuclear missiles launched at the base by the Americans, and to detonate them far enough away for the occupants of the base to survive but close enough to generate an EMP that will shut down the base's systems and release the singularities. The Doctor can then use the TARDIS to pilot the singularities through the Earth's crust, generating X-ray pulses which will sterilise Agent Yellow in the infected areas -- and kill any humans in the vicinity. To save the Earth, the Doctor must kill millions.

Chris and Jason set off with Benny, who is starting to show the first signs of infection, but they are captured by Tammuz, who has killed the soldiers pursuing him and taken their force field generators. He still does not believe the extent of the disaster he has unleashed and is convinced that the Americans are stockpiling weapons for use against his people. Tammuz attacks them, trying to stop Chris from re-arming the bombs, and as Benny and Chris fight him off it's left to Jason to press the final button -- although he knows that in doing so he will deprive the Cthalctose ark of its power supply and end the Cthalctose civilisation for all time. As Tammuz tries to flee to safety on the surface of the Moon, the missiles detonate, baking the dust into a sea of glass in which they are all trapped. Tammuz is sucked away into a singularity when it emerges from the surface of the Moon, and as the Doctor pilots the singularities through the Earth, killing a tenth of the planet's population, Chris -- who has been in a state of shock all this time -- realizes that Imorkal planted the formula for the antidote in his mind as well.

With Chris' help, the Doctor corrects the errors in his previous work, saving the Earth from any strains of Agent Yellow which survived the singularities, and saving Benny and the remaining villagers as well. But Benny and Jason realize that they can no longer live with each other, and agree to divorce. Jason remains on Earth to help deal with the aftermath of the disaster he created, while the Doctor and Chris take Benny back home to the 26th century.