Seven-eighths of the planet Hitchemus is covered in water, and human musicians have built a colony city over the top of ancient alien ruins on the sole island continent. According to the tourist guides, the planet experiences year-round clement weather, but in practice, the Doctor and his companions find it subject to sudden, frequent squalls and storms. Nevertheless, the Doctor and Fitz soon settle in; Fitz makes a comfortable living busking, while the Doctor joins an orchestra conducted by Karl Sadeghi. For over a century, the Doctor has had a tune going through his head, and he hopes that playing the violin in Karl’s forthcoming concerto will help him to find out what it is. Meanwhile, Anji visits the standard tourist areas and meets Besma Grieve, a xenologist studying Hitchemus’ native animals; while similiar in appearance to the Terran tiger, their intelligence varies with each generation. The last generation of tigers were beasts, and the colonists used to hunt them for sport and experimentation; however, the current generation of tigers is at least as smart as gorillas. Or so it appears. But one day, while looking for economics texts in the city library, Anji finds herself stalked by a tiger -- and nobody believes her when she claims that it stole a book from the shelf before her eyes...
Karl is both fascinated and disturbed by the Doctor, who plays the violin like a virtuoso, has spotty memories of taking piano lessons from an angry deaf German, and knows the perfect recipe for chocolate martinis. He doesn’t really fit in with the orchestra, and soon after Anji’s experience he finally goes too far, playing wildly in one rehearsal and leaving the others far behind. Karl demands that he learn to fit in, but the Doctor refuses, insisting that he hears something in the music which even Karl, the composer, can’t perceive. Frustrated, Karl accuses the Doctor of using his superior talents to parrot the moves of a virtuoso with none of the feeling, and in a fit of rage the Doctor smashes his violin against the wall. Karl kicks him out of the orchestra, and the Doctor returns to his flat with another violin to play his music alone. Fitz tries to mediate, knowing how much the concerto meant to the Doctor, but suddenly everyone in town has something far more important to deal with, as hundreds of tigers pour out of the Bewilderness and into Port Any. They are much more intelligent than the humans ever suspected, and they have the element of surprise. Within hours the city is theirs.
The Doctor snaps out of his sulk, and broadcasts a public message with a hidden clue drawing potential resistance fighters to a rehearsal hall. One of the potential rebels, Ajamu Quick, is a former military officer, who intends to make a series of co-ordinated quick strikes to keep the tigers off balance; however, the Doctor would prefer to try communicating with them first, as Hitchemus is the tigers’ world and they may just be defending it from the invaders who hunted their ancestors. The tigers have been feigning stupidity for some time, and with the help of vocoders to make the proper sounds, they can speak the human language fluently; but only the Doctor can speak theirs. The tigers are apparently taking hostages, all of them music teachers, and although the Doctor tries to lead a party to rescue them he is forced to retreat, with a few casualties, when the tigers threaten Karl’s life.
Anji and Fitz try to rescue Besma, and barely succeed; pursued to the garden shed by an angry tiger, Anji panics and runs it through with a pitchfork, nearly killing it. Meanwhile, the Doctor helps the Movement to retake the spaceport, but they find that the tigers have removed the computer’s software module; it will take them weeks to repair the damage and contact help. Quick refuses to negotiate while the tigers are holding hostages, and reveals that he has modified the Movement’s tranquiliser guns to deliver lethal doses. The Doctor, disgusted, goes out to speak to the tigers himself, but he doesn’t tell Quick and the others, who see him with the tigers, misinterpret what’s happening, try to rescue him and provoke a bloodbath. Quick blames the Doctor for the deaths, and the Doctor realises that the Movement is listening to Quick, not him; this is their city, and the Doctor is an outsider. Furious, the Doctor gives up on them completely, leaving Anji and Fitz to keep matters under control in the city while he tries talking sense into the tigers.
Out in the Bewilderness, the Doctor meets a potentially friendly young tiger named Bounce, and after they survive a hurricane together she agrees to take him to the other tigers. The Doctor manages to convince their leader, Big, that he believes the tigers and humans can find common ground; at the moment, each species fears the other and believes they have to be in charge to get what they want, but the Doctor is sure this can change. Big claims that the tigers only want to learn the human concept of music, and allows the Doctor to see Karl. The Doctor is enraged to see his friend half-starved, traumatised and suffering from exposure. The tigers have been keeping the music teachers separate so they can’t conspire together, and have been feeding them flowers and raw meat. The Doctor demands of Big that the tigers provide their teachers with proper food and medical supplies, to convince them that the tigers genuinely want to learn instead of trying to force lessons out of them. He realises that many of the tigers are living in the moment without considering the long-term consequences of their actions, and when he confronts Big about this, Big decides to show the Doctor what it really means to be a tiger on Hitchemus. The Doctor already has one enemy amongst the tigers; Longbody, who knows that the next generation will be animals again, and doesn’t see why she should waste her time planning for the future when the human invaders pose a threat here and now. The fact that she nearly died already, when Anji stabbed her with a pitchfork at Besma’s, just convinces Longbody that she’s right...
Besma and a few remaining music teachers are hiding out beneath the University, but Besma is going stir-crazy. She thus convinces Anji to take her to the Stela, an old alien ruin some distance away; the tigers occasionally visit it, and Besma, who can’t believe that the tigers successfully hid their intelligence from her for so long, has concluded that the Stela is a mind-altering machine which has caused the change in the tigers. Quick is more interested in harassing the tigers than in finding the cause of their intelligence, so Fitz helps to smuggle Anji and Besma out of the city. Anji eventually begins to believe that Besma is only grasping for an explanation, but she and Besma have only started to make notes and theories on the Stela when the Doctor and the tigers arrive, forcing Anji and Besma to hide in a nearby cliff.
Unaware that Anji and Besma are nearby, Big shows the Stela to the Doctor, who realises that it’s a combination lock based on the tigers’ written language. But is is meant to be a puzzle which only intelligent tigers can break, or did the designers not realise how much knowledge would be lost between generations? When the words on the Stela are shifted into the proper position, a door opens up into an underground chamber -- a storehouse of knowledge recorded by past bright generations for their descendents. Big reveals that the tigers wish to learn about human music, so they can add knowledge to the storehouse for future generations. Fascinated, the Doctor explores as much of the storehouse as he can, and finally realises that Hitchemus’ climate is not going wrong -- not as the humans understand it. The planet’s axial tilt and distant moon should naturally result in wildly changeable weather, and the fact that it’s been mild and gentle year-round until now suggests that a previous generation of tigers found a way to control the planet’s climate. And the change in the climate suggests that the network is now going wrong.
The Doctor offers to teach Big’s people how to open the other doors of the storehouse to regain more of the knowledge they have lost, on the condition that Big release the music teachers as a show of good faith. Big agrees to do so, and the Doctor opens the door to what he believes to be the weather control room. Doing so triggers an earthquake, and Big sends Longbody to the surface to investigate -- but Anji and Besma have just emerged from hiding, and when Longbody emerges from the storehouse the first thing she sees is the human who nearly killed her. She attacks Anji, killing Besma when she tries to intervene. Big stops her from killing Anji, and although the Doctor stops the other tigers from closing in on Anji, Anji, shocked by Besma’s sudden and violent death, doesn’t see that. All she sees is that the Doctor is speaking the language of the tigers, and that he has failed to react to Besma’s death. When he enthuses to her about what he’s learned from the storehouse, she concludes that Besma was right; it’s an alien device for altering the mind, and it has affected the Doctor. She leaves him with the tigers, and returns to the city, planning to tell Quick about the Stela so the Movement can blow it up and put the tigers, and the Doctor, back to normal.
Opening the weather room has caused an array of metal fins to slide up out of the ground, all over the continent. In the city, Quick has been planning a raid on the spaceport, which Fitz knows will get people killed; in order to delay him for a while, Fitz has suggested holding a morale-building concert first. The concert is interrupted by the rising of the Nodes, and when Fitz and his friends study one they discover that it is transmitting radio signals -- and it apparently puts them in contact with a human spaceship on its way to Hitchemus. There is now no need to raid the spaceport, but just as Fitz is congratulating himself, Anji arrives with her plan to blow up the Stela. In any case, the voice on the Node was not that of a human, but of Longbody, who realised what was going on when a Node near the storehouse began transmitting and used a vocoder to trick Fitz and his friends. Believing her to be a crewmember of a human ship, they are now revealing all of the humans’ plans to her. She is gradually building up a following amongst the tigers, some of whom agree that the humans must be dealt with at once; but she is not yet ready to act against the Doctor, not until she manages to prove to Big that the Doctor is their greatest threat.
The tigers allow the kidnapped musicians to assemble an orchestra, but Karl, traumatised by his experiences, leads them in an act of defiance, smashing apart their instruments and refusing to play. Just as the tigers are about to kill them all, Big’s messengers arrive to release them as the Doctor had requested. Karl insists upon being taken to the Doctor, who has just found another recording proving that there is a second storehouse buried beneath Port Any; raising it would destroy the city, but the Doctor believes he can find another way in. At the Doctor’s urging, Karl teaches the tigers’ first appreciation class, playing a recording of Beethoven’s Fifth and showing them how to pick out the recurring themes of the piece. The Doctor believes that with a little coaxing, the tigers and humans can learn to co-exist peacefully. Sadly, he has overestimated Karl, who has been starved, exposed to the elements, and forced to watch as the tigers ate the body of the woman who was killed during the Doctor’s earlier rescue attempt. Whatever the Doctor may think, Karl would gladly see the tigers all dead.
When Longbody learns how Karl feels, she finally tells Big that she’s tricked the humans into revealing their plan to destroy the storehouse. Rather than turn on the Doctor, however, Big gives him an opportunity to choose sides -- and to Karl’s horror, the Doctor chooses to help the tigers protect the storehouse. The storehouse is only in danger because they allowed Anji to live, but the Doctor will not allow them to harm Karl, and Big agrees to let Karl live -- as a hostage to ensure the Doctor’s co-operation. However, he won’t allow the Doctor to contact the Movement; instead, he allows Longbody to send a stripe of tigers to the city to search for the bomb. Longbody chooses the ones who think the way she does, and when they arrive in the city they begin to kill almost everyone they encounter, telling the terrified survivors that the Doctor sent them...
Despite what he’s promised, the Doctor slips away from the tigers and uses the Nodes to contact Fitz. The storehouse is the tigers’ equivalent of the Library of Alexandria; destroying it would deliver their culture a blow from which it will never recover. Fitz warns Anji of the truth, but they are too late to stop Quick from launching the bomb, a remote-piloted hovercar packed with explosives. By this time, however, the Doctor has learned enough about the weather control system to whip up a thunderstorm, and as Big and Longbody watch in awe, he strikes the approaching bomb out of the air with a bolt of lightning. He’s saved the tigers’ civilisation, but Longbody knows that he did it for his own reasons and trusts him no more than she ever did. And a camera aboard the hovercar has broadcast the Doctor’s part in its destruction back to the city. Fitz knows that the Doctor was just trying to save the humans from their own mistake, but Quick believes that the attacks from Longbody’s stripe are a precursor to a mass attack... and that the Doctor has gone over to the tigers’ side completely.
The Doctor may grasp how to manipulate the local weather, but he can’t work out how to control it on a global scale, until Bounce wonders aloud why the record of the second storehouse was located in the weather room. The Doctor realises that the global controls must be located in the second storehouse -- but one of the younger tigers play-cuffs the Doctor a bit too hard in his enthusiasm, knocking him out for hours. When he awakens, he realises that he doesn’t fit in amongst the tigers any more than he did amongst the humans. By now Bounce is convinced that the Doctor will save them all, and she agrees to help him free Karl and return to the city, to find a way into the second storehouse before anyone else. The city appears deserted when they arrive, as Longbody’s stripe has driven most of the humans into hiding; fearing for Bounce’s life, the Doctor tells her to go back out to the Bewilderness and wait for Big to send more of his followers here. In the meantime, he takes Karl to his apartment to rest; Fitz is relieved to see them back, but Anji still blames the Doctor for walking out on them and refuses to speak to him. Karl refuses to let the Doctor leave without him; this is his world, and he will stand by the Doctor and fight to protect it. However, the Doctor fears that Karl really just wants to see the tigers suffer as much as he has, and thus doesn’t tell him about the ace he holds literally up his sleeve -- a portable armband which he stole from the storehouse, and which is linked to the weather control systems.
The next day dawns without tap water, as Longbody’s strip has seized control of the dam; the Doctor thus theorises that the entrance to the second storehouse must be located beneath it. The Doctor returns to the Movement’s hideout to confront Quick, but learns that Anji and Fitz have told him about the second storehouse -- and that he plans to destroy it. The infuriated Doctor storms off with Fitz and Karl, intending to get there first. Anji wants no part of this any more, and she returns to Besma’s house to read through her notes and try to make sense of what’s happening. She concludes that the tigers’ intelligence has always varied like this, perhaps as an evolved adaption to their planet’s changeable weather conditions; smart and dim generations alternating, with the occasional flowering of full intelligence. Knowing that the Doctor is the only person who will listen to her, she sets off to find and tell him, but as she goes, the siege mentality of the city snaps at last; after days of terror, the humans finally emerge from hiding and start to fight the tigers. Soon the entire city is at war.
The Doctor, Karl and Fitz find that more tigers have arrived at the dam; Big has realised that Longbody is calling all of the shots in the city, and has finally sent his own people in. The Doctor bluffs his way past, claiming that the humans have planted bombs in the dam, but once inside the control room he barricades the door. The tigers have burrowed through the floor to get to the storehouse, but have been unable to open it yet. The Doctor tries to do so, but the tigers, realising what he’s doing, begin smashing through the wall of the dam to get to him. Karl, fearing that they will tear the Doctor apart, gives in to his hatred for the tigers and opens the dam’s floodgates, unleashing tonnes of water upon the tigers and sweeping them away. The Doctor, enraged, forces Karl to look at what he’s done -- he has crushed and drowned dozens of tigers, and Bounce may be amongst them. The Doctor sends Karl and Fitz to shelter in the hydroelectric plant while he tries to repair the damage, and Karl has no choice but to leave, knowing that he will never be able to make amends for what he’s done.
Anji finds the Doctor and tells him what she’s learned, and when Big and Longbody confront the Doctor over the carnage in the creek bed, Anji finally realises that she can understand their language; as a member of the TARDIS crew, she could have done so all along, but she never let herself listen properly. Big orders the Doctor to open the storehouse so the tigers can drive the invaders off their world, and the Doctor agrees to do so. However, Fitz has been watching from a distance, and he creates a distraction, enabling Anji to escape while the Doctor enters the storehouse and locks it behind him. Enraged, Longbody pursues Fitz to the power plant, where she is tripped up at last by her contempt for the humans; she never bothered to learn how electricity works, or what the warning signs plastered about mean. Due to the tension between the humans and tigers, the plant has not been fully repaired after the hurricane, and Longbody electrocutes herself when she brushes up against a damaged machine while chasing Fitz.
Karl is shivering on the roof of the power plant, trying to think of a way to put things right, when the skies cloud over and another hurricane forms. The Doctor walks out of the storehouse, surrounded by a nimbus of lightning, and after sending a miniature tornado through the crowds of battling humans and tigers to get their attention, he uses more tornadoes to evacuate the spaceport and strikes it with lightning, releasing all of the concentrated power of the storm he’s just created. The spaceport is reduced to ashes; it’s still possible for human ships to land on Hitchemus, but now it’s more trouble than it’s worth. The winds carry the Doctor’s voice to all corners of the city as he informs the stunned tigers and humans that he’s also caused the weather control system’s gradual decline to get much worse. The tigers and humans now have no choice but to put aside their differences and find a way to work together; if they don’t, then the island continent will be underwater within a decade.
That is the end of the war; even Quick and Big can tell when a fight’s over, and although there will still be bitterness and hatred on both sides for some time, they agree to work together to keep the peace. Anji finally realises that the Doctor never changed at all, and although she still doesn’t fully trust him, she decides to keep travelling with him. Later, Karl finds Fitz playing an unfinished song he once wrote about the Doctor; although neither of them knows it, it’s the same tune which the Doctor has been trying to remember for over a century. Karl tries to apologise to the Doctor for his actions, but he knows that he’s missed his chance to make amends. He will have to remain on Hitchemus to repair the damage he caused, while the Doctor and his friends continue on to further adventures elsewhere. The Doctor will not be playing in Karl’s concerto; he’s found his own music at last.