Sontarans invade the planet Jekkar, and an unfortunate smuggler named Kurt, who left it a bit too late to flee from the authorities, ends up in jail with a wandering scholar named Smith. Commander Steg suspects Smith of being a spy, and he sentences both Kurt and Smith to death to serve as an example of the Sontarans’ swift military justice. But before their execution, Smith reveals to Kurt that he’s organised the native Jekkari into an army to fight the humans who had invaded their world; they can just as easily turn those new skills against the Sontarans. The Jekkari help Smith and Kurt to break out of jail, and Kurt takes the opportunity to flee the planet, vowing to use the proceeds from this venture to go straight -- and owing a great debt to the strange little man called Smith, who told Kurt just to call him “the Doctor”.

Some time later, two strangers named Cwej and Forrester arrive in Megacity, the corrupt capital of the mining world Megarra. They’re looking for someone, and the city’s criminal kingpins of the city need to know who, and quickly. The police chief, an intellectually augmented Ogron named Garshak, brings them in for questioning, and they explain that they’re detectives on the trail of a serial killer who targets the rich, steals their identities, and kills again when the money runs out. As the city’s kingpins are the killer’s most likely targets, Garshak releases Cwej and Forrester to continue their investigation -- but by this time they’ve been targeted for death by a Sontaran intelligence officer, Gorsk. Roz and Chris track down the “Ripper” to a popular nightclub, but are too late to prevent the alien killer from murdering the nightclub’s owner, Raggor; however, they do interrupt it before it can take on Raggor’s identity, and it is seriously injured in the gunfight which breaks out when it tries to flee. The killer escapes when Roz and Chris are attacked by a pack of Wolverine assassins hired by Gorsk, but Garshak and his men arrive and save them. The Ripper has already booked passage to Space Station Alpha under his old identity and left the planet, but Garshak sends Roz and Chris after him, reasoning that Megacity will be better off without them. Gorsk reports the incident to Sontaran High Command and kills the Wolverine leader for his failure, but he is then caught and killed by the remaining Wolverines.

Meanwhile, at the Doctor’s request, Benny visits the university on the planet Sentarion -- a world populated by a race of giant insects -- to research the background of the Sontaran/Rutan conflict. Upon arriving she is nearly killed by an assassin from the Harrubtii sect, and although her guide dismisses the attacker as a mere bandit, the university Chancellor -- an old friend of the Doctor’s -- lets slip that the Harrubtii are in fact the planet’s religious zealots. Benny settles in to begin her studies, only to find that far more has been recorded about the Sontarans than the Rutans. That night she goes out on the town with Professor Lazlo Zamar, a visiting scholar who has a little too much to drink and tells her that he’s researching the Sentarii religion itself. He believes that they were uplifted by another alien race, and that the process is still going on. Before he can expound upon his theories the Harrubtii descend upon the café and kill him, and when Benny tries to report the incident, she finds that it’s being covered up at the highest levels. Convinced that Zamar’s theories led to his death, Benny investigates on her own, and eventually discovers that there is an area of the University which outsiders are forbidden to enter -- the Temple of the Shining Ones. When she arrives to investigate further, she finds the temple apparently unguarded, but when she enters she learns too late that the Harrubtii allowed her to trespass on sacred ground in order to give themselves a pretext for killing her. The Chancellor arrives at the last moment, and out of respect for his friend the Doctor, he refuses to let the Harrubtii kill Benny on sacred ground... which means that she must remain in the temple for the rest of her life.

The Doctor travels to the Rutan homeworld to deliver a warning. While on Jekkar he learned that the Sontarans have discovered one of the Rutans’ greatest secrets, and that they intend to take advantage of it to launch a major assault. The Rutan agent formerly known as Karne, whom the Doctor believed to be dead, has in fact survived and is trying to reach its homeworld to deliver its own warning. The Rutans claim that there is no such secret, but as the Doctor tried to warn them of the danger, they allow him to leave their homeworld alive. Meanwhile, the Sontarans are forced to retreat from Jekkar thanks to the natives’ guerilla tactics, and although Commander Steg faces possible disgrace for his failure to hold the planet, Admiral Sarg does not punish him, knowing that the Doctor was responsible. The Sontarans are nearly ready to act on their discovery, but Karne must be prevented from warning the Rutans ahead of time -- and the Doctor must be prevented from helping him. Sarg places Steg in charge of the mission to find and kill Karne, the Doctor, and the Doctor’s companions.

Karne arrives on Space Station Alpha, but he’s still suffering from the injuries he received on Megarra and immediately starts to look for a way off. The first ship scheduled to depart is the solar yacht Tiger Moth, captained by Lisa Deranne and funded by a syndicate consisting of the famous fashion designer Zorelle and the rich, young and beautiful Mari and Nikos. Lisa’s fourth backer pulled out at the last moment, but fortunately a shady character named Kurt hears her complaining in the bar, and agrees to take his place, ensuring that Lisa will be able to enter the forthcoming competition after all. Karne then contacts Lisa and offers to pay her for passage away from Alpha, and when she turns him down, the Rutan slips into her ship anyway and hides in the engine room, drawing power out of the engines to heal itself. Unaware of the danger, Lisa and her backers depart from the station on schedule. Shortly afterwards, Roz and Chris arrive and are reunited with the Doctor, but as they plan their next move, a Sontaran War Wheel arrives in response to Gorsk’s final transmission. The Sontarans blast away the cargo hold with a warning shot and seize control of the station, but they soon determine that the Rutan is no longer aboard and set off to track down all of the ships which left the station before their arrival and after the arrival of the Megacity liner. Certain that the Rutan would have hidden itself on the first ship to leave, Steg takes personal command of the mission to capture Tiger Moth.

Tiger Moth is on a shakedown cruise, and Lisa is running her rich and bored crew through their paces when Steg arrives. The Sontarans easily seize the ship and capture its crew -- all but Lisa’s engineer Robar, who was investigating the drain in the engine room at the time. Robar is attacked, killed and duplicated by the Rutan, which then kills a Sontaran trooper and attempts to board the Sontarans’ vessel. Its disguise is penetrated, however, and it flees from the Sontarans back into the depths of Tiger Moth. Steg places the airlock under guard to prevent the Rutan from escaping, and takes Lisa to see Robar’s body to prove that they have a common enemy. Lisa agrees to help him find the Rutan.

Steg has failed to recognise the older Kurt from Jekkar, but Kurt has recognised Steg, and he knows that the Sontaran will break his promise to spare the crew of Tiger Moth once his mission is complete. When Steg returns to tell the others of Lisa’s decision, Zorelle, trying to curry favour with her captors, reveals that Kurt tried to convince them to turn on the Sontarans. Steg offers to let Kurt take his gun and shoot him, but Kurt turns down the offer; however, Nikos then grabs the gun and tries to shoot Steg, only to find that the gun wasn’t primed. Having located the troublemaker amongst his captives, Steg kills Nikos, and Lisa is forced to sedate the hysterical Mari. Zorelle accompanies the others out to hunt for the Rutan, but loses her nerve and returns to the crew’s quarters -- where the Rutan, which has killed Mari and taken her form, now does the same to Zorelle.

Lisa agrees with Kurt’s conclusion that Steg will kill them all when his mission is complete. They thus trick and kill the remaining Sontarans, pushing one into the engines to his death and stabbing Steg’s adjutant Vorn through the probic vent with a screwdriver. They then find Steg planting bombs on the airlock, but he manages to shoot and wound Kurt before Lisa shoots him. The Rutan then arrives in Zorelle’s form and boards the Sontaran ship, but the dying Steg manages to tell Lisa about the bomb in the airlock. Lisa throws the bomb into the Sontaran ship as the airlock hatch closes. With the last of his strength, Steg holds open the airlock so Lisa can return to the Tiger Moth before the airlock is opened to space. The Sontaran ship clears the Tiger Moth before exploding, and Kurt and Lisa, apparently the only survivors, limp off to Space Station Beta for repairs. It appears that Lisa will no longer be able to enter the racing competition, but Kurt reveals that he’d talked the others into making the syndicate a tontine; as the only survivor, he can afford to bankroll Lisa’s entry into the yacht race all by himself.

Back on Space Station Alpha, the Doctor waits for the Sontarans to spread their forces thin searching for Karne, and then leads an attack on the few remaining on Alpha. The attack is successful, but he then discovers that the Sontarans’ first “warning shot” sheared away the cargo hold where the TARDIS had materialised. In the aftermath of the attack, it could take weeks for a salvage crew to recover it. The Doctor, Chris and Roz thus board a ship to Space Station Beta to ponder their next move, and once there they meet Kurt and Lisa. Kurt recognises the Doctor at once, and when they share stories, the Doctor is upset to learn that Karne is dead; if he fails to deliver his warning and the Sontaran attack succeeds, the stalemate between the two races will be broken, and the Sontarans will be free to turn their attention to the rest of the galaxy.

Rye, a curious crewman from the ship Hyperion hears rumours about the incident on Tiger Moth and slips aboard Lisa’s ship to see for himself. Some time later, his body is found aboard the ship -- but the Hyperion has already left, and the crew believe Rye to be aboard. The Doctor searches Tiger Moth’s engine room and finds a puddle of goo, proof that the Rutan divided itself in two before it attempted to escape. The second Rutan will retain all of the memories of the first, and it will still be trying to complete its mission. As the Hyperion’s flight path takes it past Sentarion, the Doctor charters Lisa to take him, Chris and Roz to Sentarion to collect Benny, intending to continue his pursuit of the Rutan from there.

Shortly after the Tiger Moth leaves Space Station Beta, Steg returns to life in the station morgue, having merely entered a healing coma in order to recover from his injuries. He summons reinforcements and returns to the War Wheel, where he reports to Sarg and accompanies the fleet to Sentarion for the final phase of the mission. The Rutan has already arrived on Sentarion, however, and when it reaches the Temple and transforms into its true appearance, the Sentarii abase themselves before their god. The Rutan orders them to shut down the Gateway and kill Benny, who now knows too much. The Doctor arrives and tries to stop the Sentarii from killing Benny, insisting that the Rutan are not gods, but the Sentarii cannot accept that; it is the Rutan who uplifted their race from savagery and established their noble civilisation. And although the Chancellor had given his word that Benny would not be harmed as long as she remained within the Temple, he cannot disobey the direct order of a Rutan.

The Sontarans land on Sentarion, and although Kurt and Lisa detect their arrival they reach the Temple too late to warn the Doctor. Steg seizes control of the Temple and orders the Rutan to open the Gateway, and although it refuses, the Doctor agrees to do so to save his friends’ lives. When the Doctor operates the controls hidden in the temple’s altar, a fracture opens in the sky, and the Sontaran War Wheel passes through. This is a natural wormhole which connects Sentarion to the Rutan homeworld; the Rutan intended to use it as a possible escape route for their Queen if their homeworld was ever seriously threatened, but now the Sontarans intend to use the wormhole to attack the Rutan homeworld itself, killing the Queen, breaking the Rutan hive mind and winning the war. But as the wormhole closes, the Doctor informs Steg that he re-routed it into an infinite loop, trapping the War Wheel inside forever. The Sentarii take advantage of the Sontarans’ distraction to attack them, and in the heat of battle, the Rutan attempts to kill the Doctor, who now knows too much to be allowed to live. Lisa fires at the Rutan just as Steg shoots him down, and her blaster bolt thus hits Steg, killing him for the second and final time.

The Doctor and his companions depart from Sentarion in the Tiger Moth, but Lisa feels that she deserves extra credit for the risks she’s taken -- and she knows just how the Doctor can repay her. The Doctor, Benny, Roz and Chris thus join Kurt and Lisa as the Tiger Moth’s new crew for the solar yacht race, and they win, securing Lisa’s future career.