Previously: The Braxiatel Collection was conquered by the Fifth Axis, which should have been impossible; Braxiatel knows the future of this sector of time and space, and this wasn’t supposed to happen. Braxiatel has been placed under house arrest and interrogated by Marshal Mushtaq Anson, who believes that Braxiatel still has access to one of his people’s time machines. Bev Tarrant formed a resistance movement, and was arrested after successfully smuggling the Collection’s shuttles off-world. Jason pretended to collaborate with the Axis, using a polymimetic fat suit to make it appear that he was personally benefiting from changing sides; in fact, he was secretly in contact with offworld mercenaries and was raising an army with which to liberate the Collection. Ms Jones unexpectedly fell in love with Bernard Moskof of Axis Criminal Investigations. Adrian and the other non-human residents were put to work as slaves, under the constant threat of being deported to the Axis homeworlds.

Isaac is dressed in an Axis military uniform and is connected to an electronic chair of some sort. At first, he doesn’t seem to recognise Benny, but some part of him acknowledges his daughter and allows her to escape. Benny takes her story to Jason and Braxiatel, and when Jason analyses the data she downloaded from the Axis communications net, he discovers that Isaac’s transmission was bounced about through a series of relays. Even Anson believes that Isaac is transmitting from the Axis homeworld, but in fact, he’s really on the planet Heaven. Benny contacts Anson and convinces him to let her mount an archaeological expedition to Heaven, claiming that its native population died out because the planet is suitable only for humanoid life forms. Anson is delighted by the opportunity to prove the Axis dogma that the Universe is designed for the benefit of humanity, and is unaware that Heaven was in fact engineered as a trap by a race of decidedly non-human life forms. Benny puts Peter in the care of the Gemayal brothers, and bids goodbye to Adrian, telling him that she loves him just in case he isn’t there when she returns. Jason convinces Anson to let him accompany Benny, and they set off with a team of Axis archaeologists -- even though the sheer coincidence of her father being the Axis military commander, and operating from the planet where she first met the Doctor, has Benny convinced that she’s walking into some kind of elaborate trap.

Joseph rescues Bev Tarrant from the Axis interrogation centre under Moskof’s nose. The Axis immediately change their security codes, unaware that the Resistance has already hacked into their communications net; the Resistance thus acquires the new codes, and under Bev, they begin to plan a major assault on the Axis. One of Moskof’s friends is killed in a Resistance bombing, and the frustrated Moskof, still quite convinced that his side is the right side in this conflict, admits to Ms Jones that he’s going to request that the alien slave workers be shipped offworld, to “clean up” the Collection at long last. Meanwhile, Braxiatel professes ignorance of the Resistance’s plans to Anson. In fact, although he’s unwilling to show it, the Occupation has Braxiatel quite rattled, but he’s unwilling to use his time machine to fight them for fear that this is just what they want him to do.

The Axis expedition arrives on Heaven, and while the archaeologists set up their base camp, Benny and Jason triangulate the source of Isaac’s transmissions -- and find that they’re coming from the Heavenite observatory where Benny first met the Doctor. As soon as the rest of the team is asleep, Benny and Jason set off for the observatory via hoverbike. Both suspect that they’re walking into a trap -- and indeed, as soon as they set foot inside the observatory, they find themselves surrounded by Daleks. They manage to fight their way past the front guard, only to find that the Daleks have carved out a secret base beneath the observatory.

Benny manages to track down her father, who has been wired into a Dalek battle computer; through him, the Daleks have taken control of the Fifth Axis military, remaking this human civilisation in their own image. Benny tries to release her father, but he blasts down both her and Jason with an electrical discharge and calls in the Daleks to interrogate them. The Daleks determine Benny’s identity and reveal that they tracked down her father in Little Caldwell by analysing the historical anomalies caused by his presence there. Once they captured Isaac, they plugged him into their battle computer in order to access his military skills and knowledge. The leaders of the Fifth Axis made contact with the Daleks after the failure of their initial expansionist phase, and the Daleks supplied them with the advanced technology and weapons that enabled the Axis to launch their second, more successful campaign. The Fifth Axis cant supports human superiority, and most of their followers are unaware that they are in fact being used as front-line troops to remake human civilisation in the Daleks’ image.

The Daleks lock up Benny and Jason, apparently intending to interrogate them separately later. Benny is furious with herself for not guessing that the Daleks are behind this; since they have limited time-travel capabilities, they were one of the few species who could have changed history and caught Braxiatel off guard. Jason then assures Benny that they can talk openly, since the sensors in his fat suit have detected no listening devices in the cell -- but it then occurs to Benny that his fat suit must contain a power source to operate the sensors, and she convinces Jason to strip down and use the polymimetic ceramaline of his suit to blow open the door. Benny, and the now naked and somewhat embarrassed Jason, return to the storeroom, where Benny destroys the sole Dalek guard with a conveniently located blasting tool. This time, she is more cautious about approaching her father, but he manages to resist the Daleks’ conditioning and restrain from blasting her down. Once she releases him from the battle computer, he returns to his old self, albeit rather weakened by his experiences.

Benny and Jason manage to get Isaac out to the hoverbikes, and they flee back to their ship, pursued by the Daleks. Fortunately, since the Axis ship’s defence technology was provided by the Daleks, it is capable of destroying the Daleks pursuing Benny, Jason and Isaac. Jason takes off, abandoning the Axis archaeologists -- and, to Benny’s horror, the Daleks firebomb the base camp on their way past, killing all of the innocent people Benny had brought along to provide herself with cover for her rescue attempt. As Isaac comforts his stricken daughter, the Daleks close in on their ship, and, realising that they might not make it back to the Collection, Benny orders Jason to send a message to Joseph so that the Resistance -- and Braxiatel -- will know the truth about the Fifth Axis.

Food riots break out on the Collection as the ordinary people finally get hungry enough to rise up against their oppressors. In the confusion, Ms Jones contacts Bev and asks her for a favour. She knows that Moskof has tortured Bev, but insists that he generally does not do this and was particularly upset with Bev because he blames the Resistance for the deaths of his friends. The time has now come for Ms Jones to choose sides, and she offers to help Bev -- on condition that she allow Moskof to live and escape with Ms Jones when the Collection is liberated. Meanwhile, Moskof announces that all alien workers are to be transferred to work garrisons on the Axis homeworlds, but Adrian and his fellow Killorans refuse to board the transport ships, and Bev’s Resistance then joins forces with Jason’s offworld mercenaries and launches a major attack on the Axis. Joseph then contacts Braxiatel as Anson speaks to him, and passes on a coded message from Jason. Braxiatel deduces its meaning, and, to Anson’s astonishment, activates the controls that are hidden inside his study. Anson has been looking for Braxiatel’s time machine ever since he arrived on the Collection, but Braxiatel has been inside it all along...

As Jason and Benny prepare to fight, Isaac realises that their ship’s navigational controls have been augmented with Dalek technology as well -- which means that, if pushed, it can outrun the interceptors pursuing them. They thus outrun their pursuers and return to the Collection, where they learn that the final battle has begun. Jason sets off to join his mercenaries, while Isaac and Benny stop off to ensure that Peter is safe and then set off to join the battle. Fortunately, the Axis officers who encounter them still believe that Isaac is on their side, and thus follow his orders without question; this begs the question as to why the Daleks would have chosen to put him in charge of the Axis, but Benny puts the question aside for the moment, and joins her friends as they fight to liberate the Collection.

The Axis officers have been expecting an attack, but thanks to Jason’s mercenaries, the Resistance proves stronger than they had anticipated. As Adrian and the Killorans prepare to make a suicidal rush on their oppressors, Braxiatel’s time machine materialises between the two sides in the form of a fence, providing the Killorans with cover. Anson escapes before they can use him as a hostage, and flees to the main control building, intending to summon reinforcements to the Collection. Jason and Adrian put aside their personal differences, as Adrian now understands that Jason was just playing along for this moment; however, Bev warns Jason that not everyone is aware of this, and his role as collaborator may later come back to haunt him. Mr Crofton, the gardener, is shot and killed by a sniper saving Jason and Adrian’s lives, but the Resistance fights through to the armoury, using Vosta’s name as a rallying cry, and prepares to storm the main control building. Meanwhile, Braxiatel watches the battle from a safe vantage point, confident that his time machine is safe now that he knows that it’s the Daleks who are after it. He’s also aware of the irony inherent in Jason leading the fight for the Collection, as Braxiatel recently erased some of Jason’s memories in order to keep the Collection safe. This is not the first time he’s done such a thing, and he’s aware that it won’t be the last...

Moskof realises that the Resistance has hacked the Axis security network and is giving out false orders. Ms Jones then contacts him and reveals that she’s prepared an escape shuttle, but Moskof refuses to abandon his post; he still insists that he’s on the side of law and order, and that it is the rebels who are the terrorists. He and Ms Jones are then spotted by an angry mob, and Moskof, fearing that they will kill Ms Jones as well, pretends to take her hostage, claiming that he was only ever using her to get leverage with the staff of the Collection. The angry mob doesn’t buy it, but Isaac and Benny arrive before they can lynch Moskof and Ms Jones. They offer Moskof a chance to surrender, but he refuses to accept their “justice,” and Isaac is forced to shoot and kill him when he opens fire on them. Isaac leads the others away as Benny consoles the grieving Ms Jones; later, when she is reunited with Adrian, he promises to see that Ms Jones is protected from retaliation.

The few remaining Axis troops are holed up in the control centre, but they’ve armed themselves with Dalek weapons, which Anson believes to be experimental new weapons developed on the Axis homeworlds. Isaac then suggests using Braxiatel’s time machine to transport the Resistance directly into the control centre, and Braxiatel is rather embarrassed to realise that he’d overlooked this possibility. Unfortunately, as soon as the resistance fighters have boarded the time machine, Isaac slips into a trance and operates the controls, piloting the time machine into a Dalek time corridor. Too late, Braxiatel realises that Isaac is still under Dalek control; though they have limited temporal technology, they’ve always sought the full power of Braxiatel’s people, and they set up Benny’s father on Heaven and arranged the occupation of the Collection all in order to lure Braxiatel’s time machine out into the open and get Isaac on board. Braxiatel has walked right into their trap, and now a Dalek time machine is closing in on his ship.

Braxiatel loses his temper and attacks Isaac, waking him from his trance. The others pull Braxiatel off the recovering Isaac, and Benny suggests that they resume their original course; the Daleks will assume that they’re trying to escape, but in fact, they’ll be leading the Daleks right into the Axis control centre. Braxiatel does so, and when the two time machines materialise and the Daleks emerge from theirs, Anson concludes these aliens are allied with the Resistance and orders his men to open fire. The Daleks thus find themselves under attack with their own weapons. Isaac emerges from Braxiatel’s time machine, still playing at being the Axis’ military leader, and takes command of the fight. Anson retreats, either to call for reinforcements or to save his own skin, but he is cornered by a Dalek, which seems to enjoy revealing that the Fifth Axis is just a front for the Daleks before exterminating the horrified Anson.

The Fifth Axis soldiers destroy the attacking Daleks, and Isaac then orders the few survivors to surrender to the Resistance. Braxiatel then wires together bits of the two time machines to create a device similar to the Dalek battle computer, and when Isaac takes his place in it, he finds that he is once again in charge of the Fifth Axis military computer network -- but this time, with his own mind. Since Benny is the one who lived through the worst of the Occupation, Braxiatel asks her to decide what to do next -- and she tells her father to wipe out the Axis. Isaac gives out a series of orders sending the various Axis fleets into black holes, causing them to attack their own homeworlds, or leading them into ambushes set by the other forces in the sector. Soon, the Fifth Axis fleets are in disarray, and the Axis is finished as a military power throughout the entire sector.