Rebel Gods continues on from Monuments. Connor, Sally, and Locky have not noticed any signs that the newly-freed Rebel Gods are interfering with humanity, but they are still on guard. Over a dinner Connor doesn't need to eat, because he is now a god, he discovers his mother Eleni has started dating again after her divorce. Connor joins Sally and explores a mysterious tunnel, which leads to Locky's basement bedroom. The trio explore a buried vault hidden on another school campus. They crack a puzzle using the former Monuments' powers, concluding with Connor activating an ancient statue to write them a coded message. Guardian Larissa translates most of the message, which shares the history of the Rebel Gods: one controlled human's fear, one controlled love, and one controlled hunger. While the god of hunger has already died, the message implores the reader to kill the remaining Rebel Gods without hesitation, or they will destroy the world.
Locky alone is troubled by the prospect of killing the Rebel Gods. As a distraction, he and Connor visit a nearby homophobic church which recently prevented the installation of a rainbow pedestrian crossing. As a prank, Locky dyes the church's lawn rainbow, like an LGBT+ pride flag, using his powers. The next day, Connor discovers Locky's rainbow lawn prank has gone viral. Larissa translates the rest of the message revealing that the Rebel Gods will seek out Connor and his friends. Sally sneaks into Connor's school and emphasises that the rainbow grass prank has made them hyper-visible to the Rebel Gods. Connor invites her to dinner with his mother, as she has been grieving and living alone. Connor's teacher informs him he has contacted Connor's mother regarding his grades and changed behaviour, which forces Connor to "come out" about being a god to her. Upon hearing of Sally's living circumstances, Eleni insists she temporarily move in with them.
The next day, Connor visits the rainbow lawn, and, amidst a throng of worshippers who believe it to be a miracle, meets Agapi, the Rebel God of love. Agapi states she has a proposition for Connor and will wait until he trusts her to discuss it. When they learn of the proposition, Locky is curious and Sally is sceptical, but they agree to meet with her on the condition that they record the conversation and play it back later, to ensure they are not influenced by her magic at the time. However, Connor lies and says he couldn’t find Yuki, Agapi's messenger cat who can contact her. In reality, he plans to return later and speak to Agapi alone. Connor spends the night delivering pizzas with the Hound-turned-ally Pete (from Monuments), who then drops him off to meet with Agapi. Agapi declares she has no interest in manipulating him. They disappear into the Parallel - the alternate dimension the Rebel Gods were trapped in. As they travel through the labyrinth, Agapi reveals she wants Connor to kill her sister.
They emerge from the labyrinth in an expensive Paris restaurant where Agapi influences a waiter to serve them for free. Connor is unsettled by the horrifying physical transformation that occurs when she users her magic. When Connor returns to Sydney, he discovers the whole night has passed and Sally is unhappily waiting for him. She accuses him of going behind her back, and criticises his plan of trusting the Rebel Gods; she wants to just kill them. At dinner with Connor's mother, he, Locky, and Sally watch security camera footage on the news that exposes Locky as the "vandal" who made the rainbow lawn. They drive Locky home to explain to his family, and learn his house is surrounded by a throng of "worshipers". They attribute this footage and public adoration to Agapi's influence. Sally tries to train Connor in physical combat to fight Agapi and the other Rebel God, Fóvos, who controls fear.
The next day, Connor and Sally travel to Locky's house and discover the worshippers have developed a cult-like obsession with Locky, finally making Connor suspicious of Agapi. He tells Locky, who is unwilling to accept that she has ill intent, as he wants to use his newfound public influence to create social changes relating to Queer People, First Nations people, climate change, and more. Later that day, Connor has dinner with Locky's family, and realises they are all under Agapi's influence. Connor realises a homophobic news anchor who has thus far resisted Agapi's charms may be under the influence of Fóvos, but when he tries to contact Agapi, he discovers the messenger cat Yuki is gone. At home, Connor finds a sheath for his sword inherited from Darroch on his bed, and a portal to Fóvos in his wardrobe.
Connor, Sally, and Locky travel through the Parallel and meet Fóvos in a North American gym, living under the name Effie. They ask her to cease influencing humans, but she claims human fears have become too dominant and destructive and that she can calm society. However, the trio dislike the implication that Fóvos is entertained by people's fears. Fóvos turns on them, amplifying Connor and Sally's fears until they are catatonic, intending to send them home with Locky as a warning against interfering with her. However, Locky kills Fóvos by willing her nerves to die, and as a result, the blue half of the labyrinth in the Parallel begins to fall apart. Locky is deeply troubled by his own actions and it is decided that Connor must be the one to defeat Agapi. At the same time, Agapi turns Locky's devoted cult into hateful rioters, and he tries to placate them with a speech. Agapi appears in the crowd, and while she is distracted, Connor tackles her into the Parallel.
Connor has a brief delusion that Locky and his mother are with him in the Parallel instead, however he realises it is Agapi's influence and breaks free. Connor kills Agapi, but the final exit from the Parallel is sealed and the whole maze is collapsing. Connor wanders the Parallel and meets a small boy who is the personification of the realm. He earns the boy's trust, realises he can reshape the Parallel, and creates a doorway out of it. Back at his mother's house, he discovers he has been gone four years. He reunites with his mother; then the next day, with Sally, who has resumed high school and finished Year 12. She tells him Locky learned how to "edit" their DNA and remove their godliness, and Connor is heartbroken that they will continue to age while he does not.
The next day, Connor visits Locky, who reveals he is still a god because he cannot edit himself, and returns Connor to being a human. Locky then tricks Connor and seals himself away in the Parallel, fearing the potential he has to manipulate humans. Connor discovers Locky's family knew and accepted this plan. However, they hope he will return. Connor visits the family every Tuesday for a long time; finally, one day, he arrives and discovers the signs that Locky has made it home. The book ends just before the pair reunite.