The TARDIS materializes on a desolate war-ravaged beach, and in his eagerness to explore the Doctor has led Jamie and Zoe into the middle of a motion-sensitive minefield before he realizes what he's doing. He manages to defuse the mines with his sonic screwdriver, but as he and his companions try to find their way back to the TARDIS they stumble across the bodies of Kalarian prisoners of war, each executed by a shot to the head. The Doctor now knows he's on the planet Kalaya and must leave immediately, but by the time he and his companions get back to where they left the TARDIS, it's gone -- and before they can search for it they are captured by a squadron of Selachians. The Selachians begin to take their prisoners to their underwater base, but the transports are attacked by a Terran Security Forces squad led by Lieutenant Kent Michaels. The transport with the Doctor and Jamie aboard is disabled, and Jamie saves Michaels' life in the ensuing battle. The humans win the battle, rescuing the Doctor and Jamie -- but the transport containing Zoe has escaped to the Selachian base.

The Doctor and Jamie are taken to the TSF base of operations to await questioning by Commander Wayne Redfern, whose name the Doctor recognizes from historical records. The Doctor learns that the TARDIS has been taken to the TSF flagship Triumph for study, but Redfern seems to buy their story that it is the Doctor's travel machine and that Zoe has the only key. As soon as the Doctor and Jamie have rescued Zoe they can be on their way -- but they must do so quickly, for the Doctor knows what the next few days hold in store. The Selachians will soon be driven off Kalaya and pursued back to their homeworld Ockara, where Redfern will drop an experimental bomb and destroy the entire planet. What he will not know until afterwards is that he has killed not only the entire Selachian species but thousands of human prisoners of war -- and if they can't rescue Zoe before the Selachians leave Kalaya, she will be one of them. Jamie, upon learning this, becomes determined to fight alongside the TSF forces and rescue her, and the Doctor, fearing for Jamie's life, decides to offer himself up to the Selachians in exchange for Zoe. However, he is discovered trying to contact the Selachians, and is arrested and taken to the Triumph for questioning.

The battle begins and Jamie's unit goes underwater, but they are ambushed by Selachians and in the fight Jamie's air lines are cut. He manages to surface in time, but the rest of his unit is wiped out, and the Selachians retreat to their ship and escape -- taking Zoe with them. On the Triumph, Redfern refuses to listen to the Doctor's attempts to convince him that there are human prisoners aboard the ship, and opens fire, trying to prevent the Selachians from escaping. The Selachians break the blockade and escape into hyperspace, heading back for Ockara, but in the confusion Zoe and her fellow prisoner John Paterson manage to escape and flee to one of the Selachians' escape pods. By the time they manage to launch it and drain it of water, however, they're too close to Ockara, and the pod automatically homes in and lands on the planet, trapping them on the Selachian homeworld. They seek shelter on an island, where Paterson hopes to find the T-Mat stations surreptitiously planted on Ockara by TSF forces earlier in the war, but they stumble across a civilian Ockaran harvesting food from the island, and Paterson beats in her head before Zoe can stop him. The Ockaran civilian's failure to return attracts the attention of the Selachian warriors, and they storm the island and recapture Zoe and Paterson.

Jamie blames himself for the deaths of his fellow soldiers and his failure to rescue Zoe, and despite Michaels' assurances that he is not to blame, he leaves the Kalayan base camp to think things over -- and is thus the first to encounter the organic weapons left behind by the Selachians to kill the human intruders while their guard is down. Jamie manages to warn Michaels, but is attacked and nearly killed by a neural scrambler -- and, against his better judgement, Michaels pauses to save Jamie's life, although this means a number of other soldiers die when he is unable to get word back to the camp in time. Jamie is taken to the Triumph to recover, along with a single Selachian captive, who was too badly injured to activate the termination protocol in his suit before he could be captured. The Triumph then sets off for Ockara, and on the way, the Doctor manages to convince Redfern to listen to him. He also meets the guilt-ridden Professor Laura Mulholland, the inventor of the G-bomb, who according to history will commit suicide within six months, sickened by what she has unleashed upon the Universe. Upon arriving at Ockara, Redfern demands the surrender of the Selachian forces, but the Selachians' Supreme Leader refuses to consider such an option and informs Redfern that he has ten thousand human captives hostage; two will be killed per hour until the Earth forces retreat.

He prepares to kill two hostages as a demonstration, but the Doctor recognizes one of them as Zoe and intervenes, identifying himself to the Leader. Before he can bargain for Zoe's life, however, Redfern cuts the transmission, refusing to make any deals. The furious Doctor points out that if the Leader is telling the truth, Redfern will be vilified back on Earth rather than given the hero's welcome he expects. Redfern is forced to concede the Doctor's point; he joined TSF in order to escape claims of incompetence following his indictment in the Interbank bankruptcy, and is desperate to prove himself a competent and decisive leader. As such, he therefore agrees to accompany the Doctor on a surreptitious mission to Ockara to determine whether the Leader is telling the truth. The Selachians, having recognized the Doctor from their historical records, make his surrender another of their demands, and keep Zoe alive in order to force the Doctor to obey them. Zoe, however, manages to escape while her guards are distracted breaking up a fight in the holding cell, and with the help of three fellow prisoners comes up with a plan of escape; she has already memorized all of the corridors she has encountered in the prison, and is certain that she can find her way to the personnel transports.

The Doctor, Redfern and a squad of soldiers T-mat to the planet's surface and head for the location of the Leader's transmission, only to find a large Ockaran settlement in their way. Redfern reluctantly goes around it, although aware that if anything goes wrong there will be hundreds of Selachians between them and their escape route. They reach the internment camp but find it too heavily guarded to enter, and are unable even to determine how many people are being held inside. Redfern, desperate to achieve something, decides to prove his determination to the Selachians by leading his men back through the village, causing as much damage as he can -- despite the horrified Doctor's insistence that the villagers are non-combatants, including pregnant females and children. When Redfern ignores him and leads the attack in any case, the Doctor breaks radio silence to alert the Selachians to their presence, and he is captured and the other soldiers killed while Redfern barely escapes with his life.

Back on the Triumph, Jamie is slowly recovering in the same medical bay as the Selachian prisoner, and he's surprised when the Selachian attempts to kill himself rather than remain a captive of the humans. Thanks to the TARDIS Jamie finds he can communicate with the Selachian, and he doesn't understand the creature's hatred of him until the Selachian describes his species' history; hunted by air-breathers who didn't believe they were intelligent, the Ockarans surgically mutilated themselves to fit into their battlesuits and drive their enemies away from their world. Ever since, they have sought to strengthen themselves so they will never be seen as a target again, and have deliberately cultivated their image as fierce warriors with no individual identity, to strike terror into the hearts of their enemies. But as Jamie hears the Ockaran language in its natural form and understands it, he realizes that the Ockarans were a peace-loving species driven to extremes by the brutal culling of their race, and understands for the first time the tragedy that is about to occur. He tells the Selachian about the planet-destroying bomb that the humans are about to drop, and they both break out of the sickbay and capture Mulholland, intending to force her to deactivate the bombs.

The Doctor is brought before the Selachian Leader to explain why he warned them of the attack after having fought them in the past. The Doctor insists that his efforts have always been to protect the innocent, and tries to convince the Leader that his species should have made an effort to show their artistic and peaceful side rather than build up their reputation as warriors; now the galaxy only thinks of them as monsters who must be exterminated. He tries to convince the Leader to release Zoe, but the Leader refuses to do so, and in his desperation the Doctor lets slip that the planet will soon be destroyed. Having gone this far he must give the Leader all the details, and resign himself to remaining in this time zone to minimise the disruption to the timelines he has caused. But although the Leader agrees to release Zoe, the Doctor must still answer for his past crimes -- and he is taken to the internment centre to await execution. He has just changed history, and he will be killed before he can put his interference right...

Jamie and the Selachian prisoner take Mulholland to the bomb chambers, but she claims she is unable to deactivate the bombs without the codes held by Redfern or Michaels. The Selachian attempts to kill her, but Jamie stops him, and Michaels then leads a team into the room, overpowering Jamie and the Selachian. Michaels then attacks Jamie, furious that soldiers died on Kalaya because Michaels was saving the life of a traitor. Redfern arrives and interrupts the fight, and while Jamie and the Selachian are imprisoned, Redfern, convinced that the Doctor lured him into an ambush on Ockara while Jamie tried to destroy his ship, orders Mulholland to prepare the bombs for launch. In the cells, the Selachian attacks Jamie for preventing him from killing Mulholland, and Jamie is forced to beat the Selachian unconscious to defend himself -- and then must hide under the bed when a squad of armed Selachians bursts into the room to rescue the Selachian prisoner. Redfern was allowed to escape in order to lead the Selachians to the T-Mat cubicles, and they have now stormed the Triumph to seize the G-bombs. Michaels fights his way to Redfern's cabin, where he finds that the bombs have been activated and are waiting only the command code to launch. There is no sign of Redfern or Mulholland, and the launch will abort automatically within seconds -- but as the Selachians burst into the cabin, Michaels gives the code seconds before the Selachians kill him.

Zoe and her fellow prisoners manage to bypass the organic weapon guarding the transport bay and locate an unguarded personnel transport, but when the Kalarian prisoner attempts to operate it telepathically he triggers an alarm. They are pursued back to the holding pen by Selachians, where their arrival triggers a riot. Zoe's fellow escapees are killed, but she is reunited with the Doctor and Paterson, and they flee to the upper levels as the Selachians, realizing the centre has been lost, trigger its self-destruct bombs. The centre turns out to have been carved out of the base of an island, and when the bombs explode the Doctor, Paterson and Zoe are able to climb out of the rent to safety. As they try to locate the island with the T-Mat cubicles, however, the Triumph drops its gravity bomb, which collapses and begins to draw the surface of Ockara towards a new centre of gravity. By the time they locate the cubicle, the planet is already beginning to break up, and Paterson remains behind to operate the console and send the Doctor and Zoe to safety. Moments later, the island is pulled away from the sea-bed, and soon afterwards the entire planet is destroyed.

On the Triumph, the Doctor and Zoe are reunited with Jamie and Mulholland, who is on the verge of a breakdown due to the use of a bomb she had nearly convinced herself would only be used as a deterrent. The Selachians have risked and lost everything to capture the G-bombs, and now their entire home planet has been destroyed -- and to avenge their species, they are taking the Triumph back to Earth to use the second G-bomb and destroy the home world of the human race. The Doctor sends Jamie and Zoe to the TARDIS while he and Professor Mulholland attempt to defuse the second bomb, but upon arriving in the bomb bays they find Redfern hiding from the invaders. The Selachians arrive and shoot Redfern before he can kill the Doctor, but before they can turn on the Doctor themselves, Mulholland climbs onto the G-bomb with a grenade which she threatens to detonate. She orders the Doctor to flee, and as the Selachians gun her down she triggers the grenade. The Doctor barely makes it back to the TARDIS before the G-bomb activates and the Triumph is crushed into a singularity. The Doctor, Jamie and Zoe escape, and the Doctor tells the emotionally drained Zoe that they can't affect the big picture -- they must be satisfied with making as many little details right as they can.