Inside the Rani's fortress laboratory, her Lakertyan servants Beyus and Sarn place the unconscious body of Albert Einstein into her collection of preserved geniuses. The Rani requires the Lakertyans' help for her experiments, outside of which she has no interest in them whatsoever. She returns to her laboratory, where the new Doctor recovers, more or less; still confused by his regeneration, he stumbles about the laboratory and, almost by accident, operates a computer which reveals that Lakertya is orbited by an asteroid composed of Strange Matter. He stumbles and falls to the floor while trying to escape, and when Sarn tries to help him the Rani angrily pulls her away, promising to punish her later for her interference. Sarn flees while the Doctor threatens to smash the Rani's equipment -- but the Rani calls in Urak, who fires an electronic net at the Doctor, entrapping him and knocking him unconscious.

Ikona enters the TARDIS and removes Mel, but as he carries her away she recovers and makes a break for it. She runs into Sarn, who's fleeing from the fortress, and Sarn, surprised, changes direction -- and runs into a tripwire. She is trapped within a force-field bubble which spins up into the air and crashes into a cliff, incinerating her. Ikona, furious, blames Mel; since she arrived from space she must be related to the invaders who have conquered his world, and now he intends to use her as a hostage in exchange for the captured Lakertyan leader, Beyus.

The Rani disguises herself as Mel and injects the Doctor with a chemical which will ensure temporary amnesia. The Doctor awakens and stumbles about the laboratory, finding a navigational guidance system distorter which could force any passing spaceships to land on this planet. He is shocked to see his reflection in a mirror, but the Rani explains that his laboratory equipment exploded, knocking them both unconscious and causing the Doctor to regenerate. He's puzzled and seems to remember the Rani's face from somewhere else, but she distracts him, breaking his train of thought, and convinces him that only he can repair the damaged equipment.

Mel tries to talk some sense into Ikona as he drags her across the landscape, but he doesn't listen to her until she saves his life, dragging him back just as he triggers another force-bubble tripwire. He reluctantly accepts that she's not his enemy, and unties her, warning her that the Tetraps will come to investigate the explosion; the other Lakertyans won't help them, as they've been completely subdued and their leader Beyus has been captured. They hear something following them and take shelter in a nearby pipe emerging from the cliff face.

The Rani is irritated when the Doctor orders her to mop his brow while he's working, and when he starts playing the spoons with his equipment wrenches. Eventually he gives up and sits moping on the stairs, refusing to do anything until he remembers what's going on, what the laboratory equipment is for, and what's inside the sealed chamber which the computer seems designed to operate. The Rani tries to drug him, but he disregards the drink and complains that his new incarnation seems to be sulky and bad-tempered. He claims that he needs a radiation wave-meter to complete his work and cheers up when the Rani suggests fetching one from the TARDIS; the Rani, who hadn't expected him to accompany her, contacts Urak, and orders him to find Mel and prevent her from interfering. Meanwhile, Beyus feeds the other Tetraps, pouring a glutinous red liquid down a trough into their lair.

The bubble-trap splashes down safely in a pond and drifts to shore, where Ikona removes the explosive bolt and casts it into the water. He takes Mel to his hideout in the cliffs where he stores some of the weapons he's captured from the Tetraps. Urak confronts them there and attempts to capture Mel, but Ikona drives him off with a firework gun and he and Mel escape.

The Doctor and the Rani have returned to the laboratory, both believing that the woman they saw on the TARDIS scanner was killed (though the Doctor still believes he was watching the Rani). He's worried by the Rani's presence on this planet and by his continuing inability to remember what the laboratory equipment is actually for -- and why was the Rani dressed just like Mel? The Rani convinces him to keep working, and eventually he discovers the problem; the wrong heat-conducting material was used, and it burned out when the computer was activated. While the Rani studies the problem, the Doctor fashions a makeshift stethoscope, places it to the sealed chamber, and hears something alive inside it... The Rani dismisses his questions and suggests using PES as a new heat shield; PHB is more environmentally friendly but would take longer to synthesize, and she knows where she can get some PES quickly. She claims she's going to fetch some from the Lakertyans, but the Doctor is puzzled; she'd already claimed that Lakertyan civilisation wasn't that advanced, and she's also shown lapses in memory -- which he's never known Mel to do before. When the Rani leaves she locks the Doctor inside the laboratory...

Ikona and Mel meet Faroon, an older Lakertyan woman who used to be friends with Ikona before he rebelled against the new order. She insists that Beyus has no choice but to collaborate in order to save the Lakertyans' lives, but Mel points out the charred skeleton of Sarn as evidence to the contrary... and learns too late that Sarn was Faroon and Beyus' daughter. The grieving Faroon continues on to the fortress to take news of Sarn's death to Beyus, and Ikona and Mel follow her and hide nearby. Mel wonders what the central ramp on the fortress is meant for, but saves the question for later; first she must break in and find the Doctor, whom she's certain will be at the centre of operations. And if the invaders need the Doctor to help them, that means something must have gone terribly wrong with their plans. Ikona agrees to lure the Tetraps away, and while the entrance to the fortress is temporarily unguarded Mel slips inside. Urak pursues but loses Ikona, but sees a red-haired woman walking along a nearby path and opens fire, trapping her in the net-gun. By the time he realizes he's captured the disguised Rani, both Mel and Ikona are out of sight. The Rani, disgusted, continues on to her TARDIS, where she fetches a panel of PES and carves it into the shape necessary for her computers.

Mel finds the Rani's laboratory, where a strange man accuses her of being the Rani and tries to overpower her. Eventually they sort out their credentials, and Mel is surprised to find that her friend the Doctor now has an entirely new face and personality. The Doctor, upset that he was so easily tricked by the Rani, realizes he's been participating in some evil scheme; the Strange Matter which composes the orbiting asteroid is a particularly dense form of matter, and if the asteroid is detonated the explosion would destroy not only Lakertya but most of this part of the galaxy. He tries to break out of the laboratory, and is aided by Beyus, who's learnt of Sarn's death from Faroon. Beyus and Faroon show him and Mel the arcade of geniuses, eleven brilliant minds kidnapped from all corners of time and space... and there's a space reserved for the Doctor.

Beyus arrives and operates the Tetraps' feeding trough, distracting them and allowing the Doctor to escape. The Doctor hides in his own alcove in the arcade to avoid the patrolling Urak, who shows only contempt for the subservient Beyus. The Doctor doesn't understand why Beyus won't help him to organize resistance, and Beyus tells him to go to the Lakertyan Centre of Leisure for his answer. Before leaving the Doctor removes the microthermistor from the Rani's computers, and is forced to overpower Beyus and knock him out when Beyus tries to stop him. The Doctor flees just steps ahead of the Rani, who discovers his sabotage and activates an alarm.

Having seen the Rani searching for the missing Doctor, Mel has sent Faroon on ahead so they won't be caught together; but when the Rani activates the intruder alarm, the Tetraps set out en masse and find Mel trying to hide from them. Urak paralyses her with venom from his tongue and has her taken back to the Rani's fortress as a hostage. The Rani orders Faroon to take a message to the Doctor...

Ikona sees the Doctor fleeing from the fortress and saves him from a force-bubble trap; he then uses a firework gun to disorient a pursuing Tetrap, which stumbles into the force-bubble itself and is incinerated. Ikona takes the Doctor to the Centre of Leisure, but warns him not to expect any answers there; the spoon-fed natives are interested only in their own pleasure and have been forbidden to speak with the contemptuous Ikona. Even his own brother, Lanisha, won't have anything to do with him. But the Doctor and Ikona soon learn why; the spinning globe in the ceiling, which Ikona had believed to be yet another pointless embellishment, is in fact the Rani's means of keeping Beyus under control. When she learns that one of the Tetraps was killed by a Lakertyan she retaliates by triggering the trap, releasing three insects into the Centre of Leisure. Three Lakertyans are stung and killed, including Lanisha. Ikona has learned too late why there has been no rebellion.

Faroon arrives with her message; the Rani is offering to trade Mel for the microthermistor. The Doctor and Ikona meet Mel and Urak at a deserted spot near the Rani's fortress, and the exchange is made... but the Doctor realizes too late that "Mel" was in fact a hologram, and he's handed over the microthermistor for nothing. The real Mel is still a prisoner, forced to help Beyus keep the computers functioning properly while the Rani stimulates her kidnapped geniuses' brain activity; she's already fallen behind schedule and is in danger of missing the asteroid's solstice.

The Doctor assumes that Mel is being held hostage to prevent him from interfering, but he has no intention of staying away. He correctly deduces that the Rani's scheme depends on timing and any further setbacks will be critical; now his first priority is to find out what's inside the sealed chamber in her laboratory. Ikona tries to distract the Tetrap guards and allow the Doctor to sneak into the fortress, but the bluff doesn't work a second time; the Doctor is captured, and paralysed by Urak's sting.

Urak suggests exterminating the Lakertyans now that they're no longer useful, but the Rani doesn't want to waste the effort until she's certain she will no longer need them. Instead, she sends Urak and the Tetraps to the Centre of Leisure with a case full of electronic bangles. Ikona follows them and watches as the Tetraps fit the bangles to the Lakertyans' legs, as the Lakertyans stand still under threat of the insects being released. When Faroon demands to know what the bangles are for, Urak gleefully demonstrates by using one to incinerate an innocent Lakertyan.

The Rani realizes nearly too late that she's overlooked one vital flaw in her plan -- the Doctor's character. She disconnects him just in time as he provokes the other geniuses in the gestalt by talking gibberish, threatening to send the brain into multiple schizophrenic seizures. While the Rani is distracted Mel removes the Doctor from his alcove, and they overpower the Rani and lock her in the Doctor's alcove herself. The Doctor then heads for the brain room, where he finds a computer with a recording of a supernova in its memory. Obviously the Rani is using the brain to calculate a formula lightweight substitute for Strange Matter, with which to detonate the Strange Matter asteroid and create a supernova...but why?

Beyus releases the Rani, who heads for the brain room and finds the Doctor and Mel close to guessing the truth. She fills in the final pieces; the force of the explosion combined with the preparations she's made in her laboratory will transform Lakertya into a Time Manipulator, a planet-sized cerebral mass capable of rewriting the order of Creation. Evolution will be restructured to the Rani's order. Urak, returning, overhears the Doctor protesting that the Rani will destroy many worthwhile species, including all those left behind on Lakertya; but she isn't interested in the fates of inferior species. At that moment the brain begins reciting the formula it has calculated, and the Doctor automatically corrects a mistake it has made -- and inadvertently provides the Rani with all she needs to complete her plans. He and Mel flee, overpower Urak with his own net-gun and escape from the fortress. The Rani isn't concerned; nothing can stop her now...

The Doctor and Mel are reunited with Ikona, who leads them to the Centre of Leisure. After studying the bangles, Ikona snaps a wire free from a fibre-optic lamp, and Mel uses it to complete the circuit on Faroon's bangle so it remains closed when the bangle is opened and removed. Faroon helps the Doctor, Mel and Ikona to remove the bangles from the remaining Lakertyans and accompanies them back to the Rani's fortress.

As the Rani's computer synthesizes loyhargil and loads it onto the rocket, the Rani prepares to return to her TARDIS to monitor the experiment... and Urak is startled when she orders him to remain behind after lift-off to ensure nobody interferes. Uneasily considering what he overheard earlier, Urak departs as the countdown to launch begins.

The Doctor convinces Beyus that the completion of the Rani's experiment will destroy his planet, and he helps the Doctor and Faroon to plant the explosive bangles around the giant brain while Ikona and Mel release the geniuses from the arcade. The Doctor cuts a circuit in the computer, and Beyus sends him and the others to safety while he remains behind to ensure that nobody interferes. The countdown reaches four and sticks, and the Doctor confronts the furious Rani near her TARDIS and informs her that the Lakertyans are rising up to overthrow her. The Rani angrily triggers the Lakertyans' bracelets by remote control... and the explosion destroys the brain and kills Beyus. But the explosion also kick-starts the countdown, and the rocket launches just as the Rani's fortress explodes. Realizing that her plan has failed, the Rani enters her TARDIS and flees before the Doctor can stop her. The delay to the countdown, however, has caused the rocket to miss its rendezvous, and it narrowly misses the asteroid.