A strange monster-related incident occurs in a rural town! A monster born from the grudge of unwanted hair attacks Fumie Sakura, a girl who lives there. Then a monster boy, O-O-O-No Shinnosuke, and his father, Daddy Little Balls, come to the rescue. They are looking for the family's mother. This was the beginning of the epic case of the monster-related problems that would ravage the town.

Fumie takes the monster father and son back home with her. Shinnosuke senses a strong monster vibe and they head to the source. They discover that the monster is not Shinnosuke's mother but a cleaning monster that uses extreme measures to declutter. Fumie, Shinnosuke and his father are tasked with getting rid of the monster at the desperate family's request.

Fumie convinces Shinnosuke and his father to form Monster Busters with her to tackle the monster-related problems cropping up around town. She tries to advertise the service to her friends at school but everyone is more interested in lunch, which happens to be curry that day. But a monster that makes everything super spicy appears and makes their curry inedible. It's a job for Monster Busters!

Monster Busters is hired to take care of a monster infestation at a normally tranquil hot spring inn in the mountain. They arrive to find that the cause of the commotion isn't monsters but a bunch of partying people, to Fumie's chagrin. But a monster flower emerges from inside the hot spring, and its pollen turns Shinnosuke and his father into party monsters.

One day, Fumie sees a single tattered monster glove walking soaking wet in the rain. She presumes that it has lost its owner and feels sorry for it. She takes it home, names it Chocolat, and tries to attend to its needs. It turns out, however, that the monster glove has other, surprising plans that evening.

Fumie hears about a camping site where people are going missing, and heads over with Shinnosuke and his dad to investigate. They follow voices coming from deep in the forest and discover a group of people who have been turned into mushrooms by the "Evil Mushroom King". The evil monster catches the Monster Busters by surprise, and they are all turned into mushrooms and truffles.

While Shinnosuke is relaxing at Fumie's home, he suddenly hears his missing mother Misae's voice calling him from somewhere. Convinced that he will find her at last, he dashes out alone and follows the voice to a deserted hospital. His mother's voice beckons him into the abandoned building, but he soon discovers that a shady monster tamer has lured him into a trap.

Fumie and Shinnosuke's dad come to his rescue in the nick of time, but Dino the monster tamer unleashes a swarm of demons that make people feel lethargic. They try to shake the demons and escape from Dino, but are far outnumbered and face certain doom. Meanwhile, Misae turns out to be closer than they think.

Shinnosuke is finally reunited with his mother and little sister, and they have quality family time for a while. He is no longer interested in fighting other monsters because he has accomplished his goal of finding his missing family and wants to go home. But Fumie wants to stop Dino from causing more trouble, and they end up arguing. Will Monster Busters go their separate ways?

Monsters suddenly overrun the town and people are thrown into a panic! The residents evacuate to a gymnasium where the Mayor addresses them and declares a state of emergency. He urges everyone to leave the town immediately, but Fumie notices that he appears to be the only one not being attacked by monsters. She follows the Mayor back to his residence and overhears a horrible secret!

The Mayor is the mastermind of the monster incidents in the town! He had hired Dino the monster tamer to chase away the town's residents in order to build a big casino. As the final step of his plan, he tries to release the most evil monster, the Monster President, from the pot where it had been sealed for centuries. Will Shinnosuke and the others be able to stop the Mayor's ambitious scheme?

The evil monster released from the pot takes over the Mayor's body and overwhelms the Monster Busters with its incredible power. Struck by the noxious substance the monster Mayor spits out, Shinnosuke's parents forget who they are and are transformed into savage monsters. Then, Shinnosuke is also struck by the substance!

Fumie's fury brings Shinnosuke and his parents back to their senses, but the Monster President emerges from the Mayor's body and shows its humongous true form. As the evil monster heads towards the town, Fumie and Shinnosuke put forth their final effort to stop it from destroying the world. The final battle between the Monster Busters and the most evil monster begins!