On the last day of the war between humans and Kaiju, a woman named Margaret Rosenblatt and a 120 ft Kaiju named Belloc fall in love, and have a son named Duncan. Sixteen years later, Margaret and Duncan are moving into a new house as he gets ready for his first day at a new school. However, Duncan fears that his orange skin and appetite for coal with make others think of him as a freak and a prime target for bullies. At school, he quickly develops a crush on its popular girl Jenna and makes an enemy out of her ex-boyfriend Troy. In biology class, Duncan makes friends with fellow outcasts, Kenny and Isabel, who happens to be a Kaiju-obssessed fangirl who develops a crush on Duncan after he shows her a gomorradon, a small frog-like Kaiju he caught in the process of apparently making a fool of himself. Late that evening, Troy's friends break into Jenna's locker and steal the money she saved for the school's Homecoming. The next day, Duncan meets up with Blitz, undercover as the gym teacher, and defends Kenny from Troy and his friends in a game of dodgeball. After a confrontation with Troy, Blitz takes Duncan to Dr. Pytel at the MEGTAF base upon the discovery of him being able to breathe fire. Later back at school, Blitz smoothes things over with the principal to keep Duncan out of trouble. While he and Troy are cleaning up their mess in the cafeteria, Isabel tells Duncan about a party that everybody will be going to, and he agrees to go in hopes of wooing Jenna.
At the party, Troy tries to tell Jenna about Duncan until his dad comes and takes him back home for being grounded. Duncan and Jenna begin to form a friendship but she abruptly leaves after he talks about Troy's dad. Isabel finds him and tells him about Jenna walking off because of the fact that her dad is dead. However things take a turn for the worst, as Belloc arrives, looking for Duncan. While hiding with Isabel, Duncan reveals to her that Belloc is his father. Belloc finds them and Duncan tells Isabel to run, but before she can escape, Belloc traps her underneath his tail. Duncan demands him to let her go and lures him away, freeing Isabel. Belloc chases Duncan but quickly captures him and takes him away to the Kaiju lair in the desert. Much to Duncan's dismay, he learns that Belloc wants him to become his successor as "King of the Kaiju" and rule over the giant monsters, though the human world has made him soft when he needs to be remorseless. Then Belloc presents Duncan as his heir to the other Kaiju and throws him into a lava pit, Duncan emerges in his Kaiju form and faints. Waking in the desert, he finds his way to Kenny's trailer. Kenny tells Duncan that Isabel told him about Belloc being his dad, and asks why he was at the party. Duncan replies that Isabel invited him, causing Kenny to become jealous. Back home with his mom, she assures him that the move and deal with MEGTAF were to let him live a normal life and go to college.
Back in school, Duncan is surprised that everyone except Troy now treats him like a celebrity. Isabel reveals that it is because she told them about he saved them from Belloc. Then Duncan sees Jenna head for the locker room and leaves. Meanwhile, Jenna opens her locker to find an envelope with a glowing crystal inside to sell and pay for Homecoming. Later, Isabel attempts to approach Duncan but loses her chance when he and Jenna meet up again. He asks Jenna to be his date for Homecoming, and she agrees. Afterwards, Blitz takes Duncan into the desert to locate the Kaiju lair but they fall under attack. Duncan fights the Kaiju while his father watches, as it is the first of many challenges for the Kaiju throne. Duncan almost kills the Kaiju but refuses to do so. Then Blitz appears with reinforcements and they open fire on Belloc, until he abruptly surrenders. That night, Duncan, Jenna, Kenny, Isabel, and Margeret go to the dance together. As Jenna and Duncan dance together, Isabel watches them despite Kenny's attempts to get her to dance with him. However after Troy and Jenna are elected Homecoming King and Queen and go on stage, Isabel dances with Duncan in a romantic embrace, causing Kenny to break them apart and unleash his fury. In the process, Kenny yells at Duncan that Isabel only likes him because of Belloc being his dad. Jenna overhears this and backs away from Duncan into Troy's arms, causing Duncan to storm out. As Isabel reprimands Kenny for what he did, two Kaiju named Abbadon and Astraroth appear.
Just as Abbadon and Astraroth start wrecking havoc, putting all the dance participants in danger, Duncan comes to their aid. Changing to his Kaiju form, he leads them into the desert and ultimately defeats them with help from Belloc, Margaret, and Jenna.