Every day on the Crooked World, Streaky Bacon the farming pig tries and fails to prevent the bizarre, bird-like Whatchamacallit from stealing his crops -- but today, as he approaches his nemesis with a blunderbuss, a blue box materialises between them and two strangers step out. Frightened, Streaky instinctively shoots the tall stranger, but instead of turning black and frazzled, the stranger collapses with a chest full of buckshot and begins bleeding. A talking ambulance speeds up and loads the injured Doctor and his friend Fitz into itself before Fitz can protest. Streaky accompanies them, but neither he nor the ambulance understand why the Doctor isn’t getting any better. Fitz tries to explain that the Doctor may die without medical attention, but on this world, people who are injured are simply whisked away by ambulances and return cured, with no intermediate steps. The ambulance eventually gets tired of waiting and kicks out the Doctor and Fitz in Zanytown. Streaky is left alone to struggle with the strange concept of “death” -- and the sickening realisation that he may be responsible for causing one.

The Whatchamacallit enters the TARDIS and “plays” with Anji, and eventually pushes the TARDIS over the edge of a cliff. Anji survives the fall and emerges to see a wolf-like humanoid fall from the top of the cliff -- but when it hits the canyon floor it simply flattens out and then reinflates itself. A pack of bizarre cars then races by, and the voluptuous racer Angel Falls suffers a blowout and crash. The gallant Sir Percival reinflates her car, and Angel offers Anji a lift -- but her racing nemesis, Dirty Duck, shoots her in the face with a water gun, and Angel crashes again while reapplying her makeup. Shaken and bewildered, Anji berates Angel for her carelessness and sets off on foot.

Fitz gets the Doctor safely to a nearby hotel, avoiding the random, wacky acts of consequence-free violence and mayhem taking place in the streets. While the Doctor rests and recuperates, Fitz turns on the TV and is surprised when the newsreader addresses him directly. He sets off in search of food, and finds the kitchen; here, the hotel cat, Jasper, is being tormented by his nemesis Squeak, a mouse who constantly sets elaborate traps to humiliate and harm him. The big fat hotel maid has ordered Jasper to get rid of Squeak, but he never succeeds -- and today he’s starting to wonder what the point is. When Fitz enters the kitchen and puts away all of the precariously balanced egg boxes without breaking a single one, Jasper realises that this man represents a different way of doing things, and tentatively follows him out of the kitchen to learn more.

Fitz returns to his hotel room to find the Doctor healing; the buckshot didn’t penetrate very far, and it vanished upon entering his chest. Angel Falls then arrives, accompanied by her guardian, a giant talking weasel named Mister Weasley. She has been thinking about Anji, and has decided that she’s tired of being harassed by an arch-nemesis who constantly tries to steal her winnings from the Races. The Doctor realises that it’s too late for him and his friends to leave; the changes to the Crooked World have already begun.

Wracked with guilt, Streaky Bacon tries to turn himself in to Zanytown’s sheriff, Boss Dogg, but Dogg orders Streaky to get back to his farm and stop wasting everyone’s time. Realising that he will not be punished properly for his crime, Streaky feels despair and tries to shoot himself -- but the blunderbuss only turns him black and frazzled, and he realises that he can’t even punish himself as he feels he deserves.

Anji gets a lift from the Skeleton Crew, a teen band who travel the country in a multi-coloured van called the Spook Wagon. Unfortunately it breaks down in Gloomy Forest, where the band flee in terror upon seeing a ghost, despite Anji’s attempts to point out that it’s clearly just a man in a sheet. The teens set a trap and capture the “ghost”, a bank robber named Gruenwald who was trying to frighten people away from the area where he’d hidden his loot -- and he would have gotten away with it too, if not for... Anji. Once the mystery is solved, the Spook Wagon starts to work again, and the Crew hand Gruenwald over to Boss Dogg and take Anji to Zanytown. However, she’s asking disturbing questions which have never occurred to the teens before. Why exactly does their van always break down in “haunted” areas? And if every ghost they’ve ever run into has been a criminal in disguise, why do they keep running away every time?

While the Doctor continues to rest, Fitz and Angel discuss her predicament, but are attacked by her enemy the Masked Weasel -- clearly Mr Weasley in a mask. When the Weasel tries to shoot Fitz with a machine gun, Fitz leaps out of the way, and Angel, standing directly behind him, is frazzled. After a moment’s stunned silence, Angel and the Weasel decide to carry on as usual, and the Weasel thus kidnaps Angel and tosses a bundle of dynamite into Fitz’s hands. Fitz tosses the dynamite out of the hotel, and it lands atop Boss Dogg’s car. When Dogg realises what he’s carrying, he slams on the brakes, and the dynamite flies off his car, landing in a passing baby carriage. The mother later finds the dynamite, panics, and flings it onto a train pulling out of town. Meanwhile, Dogg and his hyperactive nephew Scrapper lock up Gruenwald in the jail, but Dogg has noticed that the city seems quieter than usual -- as if the people are thinking about things...

Fitz asks the Doctor for advice, but the Doctor tells him to make up his own mind and deal with the consequences. Fitz therefore decides to rescue Angel, and finds her tied to on a conveyer belt heading for a buzz saw. All of Angel’s other heroes have rescued her first, allowing the Weasel to get away, but instead, Fitz attacks the Weasel, overpowers him and then turns off the buzz saw. The Weasel is placed behind bars, but Angel isn’t sure what to do in a world without her guardian. She is nevertheless grateful to Fitz, but his attempts to explain how the women of his world supposedly show gratitude are met with incomprehension. He eventually resorts to asking where babies come from, but changes the subject when she explains that married couples write a letter to the Baby Stork.

Anji is finally reunited with the Doctor and Fitz, as is Streaky Bacon, who is relieved but not entirely rid of his feelings of guilt and despair. It seems the travellers can leave now, but the Doctor refuses to do so, as he feels that they must take responsibility for the changes to the Crooked World, caused by the new ideas which they brought with them when they arrived. Boss Dogg is trying to order the people of Zanytown to pull themselves together and return to normal, but others are thinking more clearly. The Masked Weasel and Gruenwald have been locked up together, and it’s occurred to Gruenwald that they can compare notes. The shock of being thrown into jail for the first time has caused Mr Weasley to reconsider his criminal ways, but Gruenwald will have none of this, and he uses a heavy cabinet to flatten the Weasel and slip him out through the bars of the cell -- something which has never occurred to anybody before. Dogg is horrified when he finds that his prisoners have escaped, but even he can’t put into words why the changes to his world upset him so much...

Angel no longer knows her place in the world, but she is grateful to Fitz for saving her from the Masked Weasel -- and as he seemed so interested in making babies, she writes a letter to the Baby Stork for him. However, the Baby Stork is beginning to question its own place in the world, and while flying to Zanytown it accidentally drops the baby in the forest. Searching frantically, it finds a bundle lying aboard a passing train and picks it up; in fact, this is the bundle of dynamite which Fitz tossed away earlier. Fortunately, as the real baby was lost in the forest, it will inevitably be found and raised by a friendly pack of wolves.

Fitz accompanies Angel to start of the next Funny-Car Races, but not all of the contestants have arrived, as they’re starting to question the point of the races. Those who remain decide to run the race regardless, except for Dirty Duck, who lures Fitz into a trap. The villains of the Crooked World -- Dirty Duck, the witch-hag Repugna, the Masked Weasel, and Gruenwald, who now goes by the name of “the Green Ghost” -- have decided to form a consortium. Their first act of evil is to kidnap Fitz, partly to see whether they can actually get a ransom, and partly to prevent him from spreading his unique ideas of free will any further and thus taking away Gruenwald’s advantage.

The Doctor tries to convince Dogg that it’s too late to return to the old ways, and that he should instead try to teach people how to make proper choices and take responsibility for their actions. Dogg refuses to do so, and when Streaky admits that he preferred the old ways, Dogg deputizes him -- despite the fact that Streaky’s subsequent pride seems to prove the Doctor’s point. The people of the Crooked World are growing up, and while the Doctor refuses to impose his ways of thinking on them, he must accept responsibility for what he’s done to them if he wants that particular idea to catch on.

Dogg calls a town meeting to stamp out this plague of free will for good -- but not everybody agrees that this is desirable. The meeting is interrupted when Angel arrives with a TV set broadcasting the Masked Weasel’s ransom demands, and Dogg loses his temper and swears at the TV before realising what he’s done. He refuses to help save Fitz, claiming that the villains are behaving properly and that his job is only to lock them up once a proper hero does the rescuing and capturing. Though the Doctor wants Dogg to act responsibly, he sends Angel to fetch the ransom from her mansion, plotting to foil the villains. Free will is a good thing in and of itself, but the villains are abusing it to harm others -- and that’s why people like the Doctor exist to stop them.

Fitz’s captors delight in bragging about how really really evil they all are, really, and Fitz, unable to take them seriously, amuses himself by describing how villains from his planet all seek to rule the world from secret hideouts constructed inside dormant volcanoes. The Masked Weasel has had enough, and just wants to go back to the way things were, especially when the Baby Stork finally tracks down Fitz and drops the bundle of dynamite into his hands. Fitz tosses it away in a panic, and it circulates rapidly around the shack, falls into the Masked Weasel’s hands, and finally detonates, leaving him frazzled and even more certain that he’s chosen the wrong path. Fitz realises that the Green Ghost has been using the Weasel as the group’s spokesperson in order to make him a scapegoat if anything goes wrong -- and the Green Ghost may actually pose a threat, as he’s worked out that although evil always rebounds upon the evildoer on the Crooked World, the rules might be different where Fitz comes from.

Angel Falls is torn with guilt, realising that she placed Fitz in danger by dragging him out to a silly and pointless race. Anji is more interested in the million-dollar bill Angel fetches to pay off the ransom, as the use of Earth currency, dollars, supports her growing belief that the Crooked World was created rather than evolving naturally. The Doctor speaks to the Weasel through the TV and arranges to meet at an oasis outside town (actually a mirage). The Green Ghost intends to renege and kidnap the Doctor as well, but when the villains arrive, the Doctor reminds the Masked Weasel that he never reloaded his machine gun, and then drives the villains off with a custard-pie gun while he and Fitz escape by closing their eyes and running straight over the edge of a cliff to safety on the other side of the canyon. The Green Ghost, however, realises that the Doctor defeated them through sheer confidence and willpower -- which means that all the Green Ghost has to do is believe in himself, and all of his plans will succeed.

Streaky wants to return to his farm, but Boss Dogg still needs all the help he can get -- for he is beginning to remember the terrible thing that happened the last time his world was swept by changes like these. And things are about to get much worse. Jasper the house cat has been caught by the big fat hotel maid and dragged back to the kitchen, but he’s had enough of losing to Squeak, and after several more failed attempts to best his nemesis, he loses his temper -- and grabs Squeak and bites his head off. He is horrified when he realises what he’s done, but Squeak can’t be put back together, ever again. The big fat hotel maid is just as horrified, and she calls the police. Streaky is forced to lock Jasper up, and Jasper offers no resistance, but his guilt doesn’t change the fact that, for the first time ever, one of the Crooked World’s inhabitants has actually committed a real, irrevocable murder.

The Skeleton Crew contact Anji again, seeking help; since she first pointed out their world’s contradictions, they’ve started to notice them for themselves, and they now have a real mystery to solve. If free will is natural, then what explains the Crooked World as it was before? In short, where did they come from? Anji is reluctant to lead what seems to be a quest for God, but the teens explain that they really are looking for a concrete solution -- and they intend to start at Scary Manor, the most haunted house on the Crooked World, a place which all of the Crooked World’s inhabitants instinctively avoid. The Skeleton Crew just want Anji to provide an outsider’s perspective, and tell them if they are acting illogically. She agrees to help.

Boss Dogg begins arresting everyone who behaves “unnaturally”, and the Doctor decides to leave the villains to their own devices so that Dogg will learn to accept responsibility. But when a fight breaks out in the cells, a leopard is seriously injured and the Doctor realises that the changes are going further than he’d expected. A group of alley cats begin to protest outside the jail, claiming that Jasper has been demonised by a justice system run by dogs and punished for doing exactly what he was supposed to do -- unless he was expected to lose all his life and be happy about it. A crowd forms, and slowly turns into a mob. Dogg’s attempts to force the crowd to disperse are met with anger, and eventually someone throws a brick. This time, when violence erupts, it’s real violence, with real anger behind it... and real consequences. The Doctor manages to calm down Boss Dogg and remind him that this what he wanted to prevent, not participate in. A giant hologram of the Masked Weasel then appears above the crowd, who fall silent as he delivers the villains’ ultimatum; unless all their demands are met, they will use a giant laser weapon to destroy Zanytown and kill its inhabitants. As the mob disperses, numb with shock and ashamed of what they’ve done, Streaky finds Boss Dogg weeping over the body of Scrapper, who has been crushed to death by a ten-ton weight.

The Doctor realises that he and his friends have brought death to the Crooked World, and Fitz admits that he may be responsible for giving the villains ideas about world domination. Angel flees in digust from the man she thought was her hero, yet who has brought such horror to her world. However, she returns eventually, still upset but deciding that she must take control of her own life. As she and Fitz set off to search the countryside for suspicious volcanoes, the Doctor remains in town to act as Jasper’s defense counsel during his murder trial.

Despite Dogg’s attempt to steamroll towards a death sentence, the Doctor insists upon being allowed to present a defense. Called to the stand, the big fat hotel maid is forced to admit that she had ordered Jasper to get rid of the mouse for good, and had punished him when he failed. How much responsibility does she bear for the frustration which drove Jasper to this terrible act? The Doctor then calls up more and more witnesses, asking them to describe their recent thoughts and actions, and to think about how they may affect others. Streaky confesses to the pain and guilt he felt when he thought he’d killed the Doctor, and admits that he feels sorry for Jasper. The Doctor wraps up by admitting that Jasper has indeed committed murder, but suggests that there are extenuating circumstances. Unlike Dogg’s other prisoners, Jasper didn’t take advantage of the riot to escape; he has chosen of his own free will to attend his trial and accept responsibility for his crime. Now the people of the Crooked World must decide for themselves what to do about him, and how to ensure that such a tragedy never occurs again.

In the wake of the violence, Repugna and the Dirty Duck abandon the villains’ consortium. The Dirty Duck is frightened of what the good guys will do to him if Zanytown really is destroyed, and Repugna, horrified by the consequences of the riot, has decided to open a pharmacy and use her magic potions for good instead of evil. The Masked Weasel chooses to remain in order to confront the Green Ghost and atone for his own crimes, but he’s unsure whether he can stand up to the Green Ghost’s belief in himself. Meanwhile, Fitz and Angel find a brand new volcano just outside the city, sporting a sign which reads “Villains’ Secret Base, Keep Out.” Angel apologises to Fitz for her earlier outburst and asks him to demontrate this concept of “sex” he keeps going on about it. He is delighted to do so, but is in for a rather nasty surprise.

Anji and the Skeleton Crew arrive at Scary Manor just in time to see the janitor, Mr Grumper, fleeing in terror. He normally operates the parlour tricks which make the house appear to be haunted, but they’ve started working themselves, and Grumper has heard the voice of God. Anji and the Crew enter the house and are attacked by ghosts, a giant mantis, and living suits of armour -- but Thelma Brains has taught herself to see through these tricks, and she exposes them as animatronic robots and theatrical projections. The voice of God thunders out, ordering them to depart, but Thelma discovers that the voice is coming from a set of loudspeakers. In the confusion, Mike and Harmony are separated from the others, and when Anji finds them naked together in a closet she doesn’t need to wonder who introduced this idea to the Crooked World. She is, however, amused to think what a nasty surprise Fitz must have had when he discovered that the “people” of the Crooked World have the smooth anatomy of dolls.

The Doctor turns on the TV news, asks the newsreader for a live report on Fitz’s progress, and steps through the screen to join them on the mountainside. Streaky remains in Zanytown to keep an eye on Boss Dogg, but Dogg is tired of being the only one to remember the truth, and when Streaky confronts him, Dogg forces him to remember the real reason the people of the Crooked World avoid Scary Manor -- the terrible day which they have forced themselves to forget, and the reason why Dogg resists change. Streaky runs from the jailhouse in shame and grief, and by the time he pulls himself together and returns, Dogg has gone and only Jasper has seen him go.

Fortunately, Fitz told the villains to install an unguarded secret entrance to their lair, and the Green Ghost hasn’t yet worked out the logical flaw. The Doctor, Fitz and Angel enter the lair, where they hear a mysterious countdown which has stuck at “one” -- again, because Fitz told the villains that all evil lairs have a countdown which sticks at “one”. Angel is upset to encounter the Masked Weasel again, but when she gives him a chance to explain himself, he promises to turn himself in after helping to defeat the Green Ghost. Angel forgives Mister Weasley for what he’s done, realising that he never really thought about why he was trying to steal her money, just as she never really thought about why she was participating in the races. Weasley leads the others to the Green Ghost, and distracts him while the Doctor defuses the laser weapon pointed at Zanytown. However, the Green Ghost figures out what the mysterious countdown is for, and kick-starts the hideout’s self-destruct sequence. Fortunately, Fitz also told the villains that all evil lairs have a secret escape route, and he and his friends manage to locate it and follow the Green Ghost out to safety.

Despite desperate threats and warnings from the voice of God, Anji and the Skeleton Crew search Scary Manor and locate a secret passage leading to the caves beneath the mansion. There, they are reunited with the Doctor and his friends, recapture the Green Ghost, and find the remains of a spaceship’s escapd pod. “God” emerges from the escape pod and threatens them all with his divine wrath, but by now the Skeleton Crew are experienced enough to recognise a person in a mask. When they pull off God’s mask he is revealed to be Boss Dogg, who tried to impose order by forcing people to submit to a higher authority; however, the Skeleton Crew saw through the trick when they realised that “God” was “dog” spelled backwards. Streaky Bacon then arrives with Jasper, who showed him the secret exit Boss Dogg used to leave the jailhouse. Streaky orders Boss Dogg to reveal the truth, and he reluctantly does so. The people of the Crooked World were once blank slates without form or thought of their own, until the escape pod landed on their world, bringing with it a little girl and all of her colourful, imaginative and naive beliefs. The being who became Boss Dogg tried to tend to her and keep her safe, but as her beliefs spread out and changed his world beyond recognition, he came to fear that there was only one way to keep his people from destruction. Now, uncountable years later, Boss Dogg shows the others where the little girl’s body is buried.