Lucie is at home when there’s a ring on the doorbell. She opens the door and is shocked to find herself facing her old foe, the Headhunter. The woman raises an alien gun and warns Lucie that she’ll kill her if she makes a move. Lucie protests, but this is enough for the Headhunter and she opens fire. Lucie screams and the sound of her voice echoes in the air and then fades away…

Lucie wakes up and finds herself back in the TARDIS. The Headhunter explains that after shooting her, she then “un-shot” her using quantum-tipped time bullets. Despite Lucie’s protests that she’s not qualified to control the TARDIS, the Headhunter begins setting the controls. When she tells Lucie she needs her help in finding the Doctor, Lucie insists that he died six months ago. The Headhunter reveals that they’re heading for ’tweenspace’, a layer of cosmic sediment where the dregs settle. As the TARDIS begins to shake violently, she says the Universe is being destroyed and there’s only one person in all of existence who can stop it…

Far away on the ocean planet of Orbis, the Doctor is occupying his time by repairing the wreck of a tiny spaceship. He’s approached by Selta, a female of the jellyfish-like Keltan race, who tells him there’s a storm approaching, and the distraction is enough for the drive belt to snap and whip the Doctor‘s fingers. Selta can’t tell whether he’s angry as he doesn’t share the Keltans’ iridescence, but his repairs have come to an end unless he can find a replacement. He tells her that if they were on Earth he could use a pair of tights, but he’s unlikely to find any here as there are no bipeds on this planet. According to the stories told by the elders on Orbis, the Doctor was said to have come from the bottom of the sea many years ago. As they shelter from the storm, Selta asks him to tell her his story, but before he can begin, the atmospheric scanner from the spaceship starts activating. There’s just enough power left in the cells to reveal that the entire composition of the planet’s troposphere is changing. The Doctor has lived on Orbis for longer than any of the current inhabitants and he knows this isn’t normal as the storm season should have ended months ago. He believes something out in space must be having an effect on the planet.

Secretary Saccostrea approaches the elderly and rather corpulent Molluscari leader Crassostrea with important news. She interrupts his feeding and he complains that his female organs can’t hope to develop if he continues to restrict himself to a diet of photo-plankton. His temper has been fiery of late, resulting in the massacre of the Tetraploids, the firing of the murk water vents and the broiling of his crocs, and she suspects it’s because he’s keen to start breeding. She tells him she’s received word that the Barometer General’s atmospheric survey of Orbis confirms what they’d already suspected about the changes to the planet‘s environment. This will be catastrophic news for the Keltan inhabitants, but good new for the Molluscari, so Crassostrea decides it’s time to confront the Galactic Council with their findings.

Despite having read all 17 volumes of the TARDIS manual, the Headhunter struggles to operate the controls and the ship continues to be buffeted around the Vortex. Lucie explains that these volumes constitute just the start guide and the manual itself has its own library a couple of miles down the corridor. The Headhunter reveals that she got the TARDIS from the Sisterhood of Karn who’d kept it as a trophy after they teleported the Doctor out of the canyon and sent him somewhere worse. She experiments by switching the controls over to ’slingshot mode’ and they’re both thrown to the floor from the extreme g-force.

Back on Orbis, the Doctor responds to a cry for help and finds the young Keltan boy Vimix trapped in a deep well and unable to move. The Doctor summons help and is soon joined by Selta and Vimix’s bloom-father Yanos. They realise the boy must have been scrumping for barnacles again and Vimix confirms that the water came flooding in when the storm broke and he couldn’t get out in time. The group lower down some seaweed lines which wrap themselves around the boy’s limbs and then he’s heaved back up to the shore. Yanos takes the Doctor aside and tells him Vimix’s bloom-sisters have just died when the rain waters swamped the nursery pools. The Doctor is angry because he’d warned them the sea walls were inadequate. They’ll have to re-build them higher, so the Doctor suggests placing the whole town on stilts. Yanos congratulates him for the idea and says the Keltans owe him so much, but he‘s still worried the planet is turning against them. The Doctor acknowledges that Orbis is drowning, but reminds them of the time they defeated the invading Molluscari, a race of aggressive space oysters, by presenting a convincing argument to the Galactic Council by interspace radio. He’s sure they can find a way to overcome this problem too.

Secretary Saccostrea calls the Molluscari to attention for an address from their leader Crassostrea. He tells them he has great news, greater even than his conquest of the Tetraploids - his female organs are starting to develop. The oyster-like audience click their pincers in appreciation, but Crassostrea becomes angry and demands they applaud louder. Now mostly female, she then announces that the Galactic Council, a body for whom she has no respect, has considered the recent catastrophic changes to the environment on Orbis and has decided (subject to independent audit) that the Keltans’ claim to the planet is no longer tenable. This means the Molluscari claim takes precedence and Orbis is theirs for the taking…and not even the Doctor can stop them this time!

As the TARDIS eventually settles down and the two occupants recover from the effects of their journey, the Headhunter rebukes Lucie for being sick inside the control room and tells her to clean up the mess. Unfortunately the TARDIS itself is sick too, having been separated from its owner for too long. The Headhunter says she’s an old ship that‘s coming to the end of her natural life. Without the Doctor’s influence she’s leaking time waste, which is soiling the very fabric of the Vortex and rotting it away. With the Time Lords still in hiding, TARDISes are few and far between, which has inflated its value. The Headhunter has already sold the Doctor’s TARDIS, but the buyer doesn’t want an ailing vessel that’s belching out space-destroying matter in its wake, so she’s come to find its former owner so he can regenerate the ship and transfer ownership to her. Lucie knows the Doctor would never do that - but the Headhunter reveals that Lucie still has a quantum-tipped time bullet inside her brain and she’ll only remove it if the Doctor co-operates. They’re due to arrive at their destination in tweenspace in 32 minutes…

The Doctor tells Selta that Orbis’s moon is unlike any other he’s seen. Most satellites rise and wane, but this one tracks Orbis as if connected by an invisible thread that extends to a point 50 miles out to sea. Selta says there will be a funeral-feast later to celebrate the lives of the children they lost during the storm. It will follow a relatively new Keltan tradition which was formulated by the Doctor himself generations ago after he pointed out that their previous method of eating and regurgitating their own deceased wasn’t a very efficient way to compost the seabed. Selta invites the Doctor to accompany her to the dance, but before he can even change the subject, they’re interrupted by the arrival of a huge clam-ship, signifying the return of the Molluscari. Selta rushes off the raise the alarm…

As the Molluscari ship comes in to land, Crassostrea declares her intention to blast the Keltan habitation to dust. Saccostrea reminds her that the Galactic Council have not yet granted them the rights to this planet and they are only here to give the Keltans notice of their plans. They see the panicking jellyfish people massing nearby and Crassostrea prepares to address them.

Yanos is shocked to see the Molluscari return as everyone knows their claim on this planet had been comprehensively rejected years ago by the Galactic Council, but the Doctor says the Molluscari are bullies and people like that never like to be beaten. He offers to talk to the invaders and approaches the clam-ship, claiming to represent the Keltan species. Crassostrea emerges and mocks the Keltans, but the Doctor recognises her and remembers that she used to be male. He warns Crassostrea that he won’t tolerate any harassment of the Keltans, but the Molluscari leader reveals that she has in her possession a document from the Galactic Council confirming that the climate of Orbis is undergoing irreversible change and will shortly become inimical to the Keltan life. The Doctor acknowledges that the storm season shows no sign of ending, but that doesn’t mean the Keltans can’t adapt and thrive in their new environment. Unfortunately, it appears the Galactic Council don’t agree and in three day’s time the Keltan claim on Orbis will expire and be passed to the Molluscari. Yanos demands to see the document for himself, but as Crassostrea hands over the data pearl, she snaps shut her pincer and removes one of Yanos’s tentacles. Instead, she passes the pearl to the Doctor and advises him to study it well. In return, the Doctor switches on his sonic screwdriver, set to the exact pitch that will vibrate Molluscari from their shells. Crassostrea and Saccostrea retreat back to their ship in pain and seconds later the ship lifts off from the surface. Yanos is convinced the Keltans are doomed, but the Doctor urges him not to give up. Tonight they will dance and mourn their dead, but tomorrow they will start making stilts and building their town’s defences.

The TARDIS materialises and the Headhunter announces that they’ve arrived on the planet Orbis, the province of a species known as Keltans. Lucie struggles to accept that somewhere out there is the Doctor and she begins to worry about how scruffy she looks. She takes a deep breath and opens the door - only to find the ship is hovering in mid-air, several metres above a huge ocean. The Headhunter explains that the nearest land is about 50 miles away - then she pushes Lucie through the door and into the great expanse of water. As Lucie thrashes about in panic, the Headhunter says that because of the increased saline content, she should float easily, and the current will take her in the direction she needs. Unfortunately they’re in the middle of a rather hefty storm front, but she’s sure Lucie will be fine providing she keeps her mouth shut. The Headhunter closes the door and returns alone to the control room. She then proceeds to make a phone call and sends her contact a sequence of co-ordinates, telling the recipient they will be diving at dawn…

Sometime later, Lucie is woken up by a female voice calling her a “biped”. She opens her eyes and finds herself on dry land - but with a huge tentacled jellyfish standing over her. She screams in panic, but Selta pleads with her not to be alarmed and explains that she pulled her out of the sea. Lucie apologises and says she has a thing about jelly after an unfortunate incident at a children’s party in 1992. Lucie starts to complain about her sodden tights and Selta reacts instantly, recognising the word the Doctor used earlier. Without warning, she rips the tights from Lucie’s legs and runs off, claiming she needs them urgently.

The Doctor asks Lucie if they know each other. He admits that his long term memory isn’t what it was and the last 300 years or so have been a bit of a blur. He looks at her clothes and guesses Lucie comes from the 1980s, which infuriates her. She tells him they met in the early 21st century when she was dumped on him by the Time Lords on a witness protection scheme. She recounts some of their adventures and then tells him they were the best of mates, but the Doctor is struggling to keep up and thinks it‘s because he hasn‘t heard a Cockney accent for so long. Lucie slaps his face and is delighted when he says it really hurt. Selta tells Lucie she should leave, a suggestion that she readily agrees to. Once they’re alone, Selta wonders whether all Earth females are so aggressive. She turns the Doctor’s attention back to more pressing matters such as the atmospheric scanner and the mystery of Orbis’s moon. The Doctor suddenly realises that Orbis never actually had a moon before and recalls that he first saw it just a few decades ago.

The TARDIS materialises and the Headhunter emerges to be greeted by her contact, Secretary Saccostrea. They’ve never actually met before and the Headhunter rebukes the Molluscari for being late. She then refuses to accompany Saccostrea to meet their leader and insists that Crassostrea be brought to meet her.

The tights work and the Doctor starts to power up the crashed spaceship. Selta wonders if the Doctor is thinking of going back to Earth, but this just makes him laugh. She’s been thinking about what happened with Lucie and suggests the Doctor tries talking to her, but the Doctor has discovered the storms are being caused because the moon is coming ever closer to the planet. This confirms what they learned from the Molluscari data pearl. He’s sure it’s no coincidence and decides to contact the Galactic Council to see if they can persuade the Molluscari to back off. What he really needs to do is visit the moon itself, and Selta suggests asking Lucie if she knows what happened to his TARDIS. The Doctor suddenly realises that in order for Lucie and Selta to have understood each other, the TARDIS must be here somewhere, translating their speech. He races off to find his old companion.

From the safety of the Molluscari ship, the Headhunter and Crassostrea oversee an underwater expedition. The results of the search are negative, so Crassostrea insists that the whelks go deeper, even though Secretary Saccostrea warns that the pressure will cause their shells to crack. The Headhunter and Crassostrea have come to an arrangement - the Molluscari will retrieve something for her from the bottom of the ocean in return for her help persuading the Doctor leaving Orbis forever. The Headhunter has already arranged for the Doctor to be reunited with Lucie and once she gets what she wants, she’ll fulfil her side of the bargain. They listen to the screams over the communicator as the diving shoal finally succumbs to the pressures of the depths, but Crassostrea insists that Saccostrea sends down more of their people…

The Doctor catches up with Lucie and apologises, explaining that he’s had a lot on his mind recently. He asks her where the TARDIS is, and when she tells him the Headhunter has it, he vaguely recalls her as a part-recruitment consultant and part-assassin. The Doctor insists that Lucie slap him again and says that because she’s just come from the TARDIS her fingertips are still charged with chronon particles. When she hit him earlier, it reinvigorated his dormant neurons which is helping him to remember things. There’s still a lot of confusion in his head - he can remember shouting, screaming and doors being slammed - but it’s a promising start. However, Lucie is shocked when he reveals that he won’t be leaving Orbis. He says he’s happy here and he only needs the TARDIS to find out what’s happening on the moon and stop the Molluscari. Lucie insists that he’s a traveller by nature, but he tells her that’s all in his past and Orbis is now his home. Angered by this, Lucie slaps his face several times, but the sight of her apparently attacking the Doctor just causes Selta to race over to stop her. Selta reveals that bloom-father Yanos has received a message from the Galactic Council so the three of them head for town to discover what the news is.

Eventually the Molluscari’s underwater search is successful and the crew pick up the signal that the Headhunter has been searching for. She orders them to trawl the object in and then Crassostrea prepares to confront the Doctor…

Back at town, the Doctor has contacted the Galactic Council and learned that they’re not prepared to hear any appeals until six orbits have passed to allow for a cooling-off period. The Doctor tries to argue that there’s more going on here than they know and says the passage of the Orbis moon is being adversely affected by an external agency. However, the Council refuses to engage in any further discussion and cuts him off. Just then, the sound of an approaching spaceship is heard, signalling the return of the Molluscari. The voice of Crassostrea breaks in on the radio, telling the Keltans their tenancy of the planet is over. She claims Orbis for their own, but adds that in the spirit of inter-species solidarity she will allow a select number of Keltans to be transported to an artificial enclave elsewhere in the galaxy. The selection will be based on weight and breeding potential and she asks for volunteers to assemble on the beach.

The Keltans turn to the Doctor for ideas, but he says he needs more time to think. Just then, the Headhunter arrives and mocks the Doctor for being unable to save the Keltan race from extinction, despite living with them for 600 years. She tells Yanos that the Molluscari’s offer is the best one they’re going to get and advises them to take it. Lucie starts to argue with her, but to everyone’s surprise, Selta grabs hold of her and agrees with the Headhunter, assuring Yanos they have no alternative. Lucie bites her captor and is released, then the Doctor hands Selta his sonic screwdriver for protection and tells her to meet with the Molluscari and keep them talking as long as she can. Once the Keltans have gone, Lucie tries to punch the Headhunter - but the woman pulls out her gun and shoots her again at point blank range.

Saccostrea informs Crassostrea that the Keltans are beginning to gather on the shore as requested. The leader laughs and summons more clam-ships to land on the beach and begin the processing.

The Doctor tries to revive Lucie and is surprised when the Headhunter says she’s been shot with a time bullet. It’s currently burrowing its way into Lucie’s chest at a rate of one millimetre every second, but she can speed it up, slow it down or even remove it entirely as she wishes. The Headhunter tells the Doctor she’s reverse the damage and even return his TARDIS to him if he agrees to leave Orbis. However, he must also agree to switch off a device she’s extracted from the seabed. It’s encrusted in coral after resting at the bottom of the ocean for 600 years, but the Doctor recognises it as the remote activator for the Stellar Manipulator, which he took from Morbius and was holding when he fell into the canyon on Karn all those years ago. It was to protect this device that the Sisterhood transported him here in the first place. The technology can only be activated by a Time Lord, which is why the Headhunter arranged for Lucie to be brought here. She orders the Doctor to switch it off or else she’ll allow Lucie to die. He refuses to co-operate and accuses Lucie and the Headhunter of plotting this together. Until they reveal what their plan is, he intends to keep the activator safe in his pocket. Convinced that the Headhunter won’t let her ally die, he leaves them to their ‘act’ while he attends to those who genuinely need his help. Lucie cries out to him to help, but he isn’t listening…

The Great Crassostrea addresses the Keltans and says that although the five clam-ships they’ve brought to Orbis can’t possibly carry all of them, a fleet fifty times the size will shortly be arriving here as back up. As she orders her troops to round the colony up into manageable groups, she’s delighted to see Yanos turning green, the Keltan colour for fear. She reveals that green Keltans are said to make the best food, so in order to ‘prepare’ the prisoners, she gives her troops permission to terrorise them…

Still believing that Lucie works for the Headhunter, he’s not too surprised when she races out after him. She pleads with him to believe that she really is dying, but it’s only when she inadvertently reveals that the TARDIS is also dying and is belching out time waste over the Vortex that she grabs his attention. The Headhunter joins them and points out that something‘s happening on the beach and it smells suspiciously like a barbecue…

Crassostrea order her troops to be careful not to burn the Keltans with their electro-spears. She tells Yanos the Molluscari need the waters of Orbis in order to spawn, but before they can do that they need to feast. Selta protests, demanding that they release her bloom-father. She produces the Doctor’s sonic screwdriver and activates it. As the Molluscari start to vibrate inside their shells, Selta concentrates its effects on Secretary Saccostrea and within moments the woman is dead. To Yanos’s horror, Selta threatens to do the same to Crassostrea unless she honours their bargain. She activates the sonic screwdriver again - but this time the Doctor steps forward and takes the device from her hand, insisting it was meant to be used for protection, not as a weapon. Selta apologises for her actions, but it’s too late and the Doctor can’t hide his disappointment in her. Crassostrea suggests they don’t waste any sympathy over Saccostrea as she was planning on eating her later anyway.

The Doctor asks Selta to explain what she meant by “honouring their bargain“, and although she avoids the question he already knows the answer. He points out that the readings on the Molluscari data pearl were identical to those shown on the atmospheric scanner, which means they were both taken from the precise same spot on the surface of Orbis. He denounces Selta as a Molluscari agent and she explains that she was forced to help as the Molluscari had predicted Orbis faced a catastrophe that even the Doctor couldn’t save them from and had offered to save a few of her bloom-kin. She herself had already decided to sacrifice herself and stay behind with the Doctor. She pleads with him to forgive her, but he says he only wanted a friend, not someone who was devoted to him. He orders the Molluscari to leave the planet and never return.

The Headhunter arrives and points out how ridiculous the Doctor is for thinking he can hold of an entire alien army with one sonic screwdriver. She gives orders for the TARDIS to be brought out from the Molluscari ship and then Crassostrea tells the Doctor he must go and leave the Keltans to their fate. The Doctor insists that Orbis is his home now and he considers the Keltans to be his people, so he refuses to desert them. Lucie eventually joins them and is shocked to discover the Molluscari plan is to eat the jellyfish-people. Crassostrea has heard enough and orders her troops to kill the Doctor and Lucie, but the Headhunter interrupts, pointing out that the Doctor still has the Stellar Manipulator activator and he hasn’t switched it off yet.

Lucie makes an impassioned plea for the lives of the Keltans and the Doctor seems to come to his senses, finally remembering who she is and realising how much she must have suffered when she thought he was dead. He also takes the opportunity to remind Selta that he’s not really that old, considering how long-lived his race is. He admits that he long ago stopped counting the years and now tends to round his age up or down depending on which part of the Universe he’s visiting. He places the Stellar Manipulator activator in his hand and orders the Headhunter to “un-shoot” Lucie. She agrees and Lucie is returned to normal, but then the Doctor tricks the Headhunter and instead of switching the activator off, he actually increases its power.

At first nothing happens, but then suddenly there’s a huge clap of thunder and then the entire sky goes completely white. The Keltans start to scream in panic, believing it’s the end of their world, and they watch as the entire moon starts crashing towards Orbis. The Headhunter explains that the moon first appeared in tweenspace a few centuries ago when it was tiny. Since then it had been getting bigger and bigger as it was drawn to a spot 50 miles out to sea - where its controller was located. It’s not a moon at all, but the Stellar Manipulator engineered by Morbius! It’s been dormant for centuries until the Headhunter dragged its activator from the seabed and then the Doctor turned up the power. He tries to switch it off, but the controls are jammed and he can’t reverse the effect. As the oceans start boiling, the Doctor orders Crassostrea to evacuate everyone aboard the clam-ships, but it’s too late - thanks to the increase in the ambient temperature, the Molluscari leader is starting to spawn! The rest of the oyster race go into a feeding frenzy and the Headhunter congratulates the Doctor on messing things up so well.

She reveals that the Manipulator was being drawn closer to Orbis and was probably only days away from auto-igniting anyway, so all the Doctor has done is speed things up. She urges them to go back to the TARDIS, but the Doctor refuses to leave the Keltans behind. Unfortunately the effect has now become so great that the Keltans, including Yanos and Selta, start dying all around them before anyone can act. To the Doctor’s surprise, the Headhunter takes the activator and throws it into the sea where it will be destroyed along with the entire planet. Horrified by what’s happening, the Headhunter opens the door to the TARDIS and Lucie urges the Doctor to join them inside - but the Doctor says he gave up the life of a traveller a long time ago and his life here means everything to him. He knows he has to die some day and he seems prepared to accept that today is as good as any. Lucy grabs the gun from the Headhunter and shoots the Doctor with one of the time bullets.

Back in the TARDIS, the Headhunter “un-shoots” the Doctor and he instantly recovers. He’s angry with Lucie, who admits that she was acting selfishly. He tells her there are times when people don’t actually want to be saved and she should have respected his wishes, but she argues that she didn’t just do it for herself, but for Earth and the rest of the Universe. She reminds him that his sick TARDIS is destroying the Vortex, but the Headhunter laughs and admits that she made the whole story of time waste up in order to motivate Lucie. Lucie goes to attack her, but she raises the gun again and warns the girl off. The Doctor is determined to return to Orbis, but when he checks the controls he can’t find the planet anywhere. The Headhunter reveals that Orbis has been consumed by the Stellar Manipulator, but with its activator consumed too, the Manipulator has been destroyed as well. The Headhunter ignores the Doctor’s anger and points out that while he was happily living on Orbis for 600 years, someone else had to take over saving the Universe. She and her associates are getting sick of it and they’ve now decided that the Universe can’t do without the Doctor. The Doctor insists that he’s a different person now, but she says that’s a problem he needs to sort out for himself. She says goodbye and teleports from the TARDIS back to her warp ship.