Jason wakes up on a bus full of teenagers his age, 15- and 16-year-olds. Unfortunately, he has no memory of who he is or how he got on the bus. His supposed best friends, Piper — a beautiful girl — and Leo — a brilliant mechanic with ADHD — explain that they are campers at Camp Wilderness, a place where troubled teens are sent. Piper stole a BMW. Leo is a chronic runaway.
The bus stops at the Grand Canyon. The campers will spend the day learning about the area. A storm begins to brew over the canyon, and the teens' chaperone, a gruff coach named Hedge, asks if Jason caused it. The coach also tells Jason that he's never seen Jason before that morning.
The storm worsens, and Hedge orders the campers into the safety of a museum. Before Jason and his friends enter, one of the other campers turns into a ventus, or storm spirit. He throws Leo into the side of the canyon and taunts Hedge, who has taken off his disguise and has revealed himself as a faun, a creature that is half-man and half-goat.
Jason is impervious to the lightning the ventus uses to attack him. When the ventus throws Piper over the side of the canyon, Jason jumps off to save her. He catches her before she hits the canyon floor and manipulates the air to lift them back to the surface. Hedge saves Leo but is taken away by the storm spirit. A chariot appears in the sky, driven by two teenagers: Annabeth and Butch. Annabeth is furious. She had been told to come rescue three teenagers and had assumed one of them would be her boyfriend, Percy Jackson. Percy has been missing for several days.
Annabeth reluctantly takes Jason, Piper and Leo back to Camp Half-Blood and explains to them that they are demigods, children of humans and the gods of mythology. At Camp Half-Blood, they will be claimed by their god parent and begin their training so they can fight against the monsters that are sent to kill demigods. The others at Camp Half-Blood are surprised that neither Jason, Leo nor Piper has been claimed by their god yet, as that is generally done by age 13. Upon arriving at the camp, Leo is immediately claimed by Hephaestus, the god of blacksmiths and fire. Jason still has no memories earlier than that morning, but the campers notice that he consistently uses the Roman names for the gods instead of the more familiar Greek.
Piper, Jason and Leo are each assigned a guide to give them a tour of the camp. Each of them learns something interesting about the strange things happening between Mount Olympus and the mortal world.
Piper's guide, Annabeth, reveals that the gods have been unusually silent for several months. While visiting Hera's cabin, an oracle begins speaking in a strange voice. She warns Piper that unless she can free Hera by the summer solstice, the world is doomed.
Leo discovers that a mechanical dragon, built by a child of Hephaestus, has gone haywire and is attacking mortals in the woods. The other demigods have tried to trap it, but it has evaded them. He also learns that no child of Hephaestus has been born with power over fire in hundreds of years. Since bad things usually happen when such a child is born, Leo doesn't admit that he has the ability to control flames.
Jason is brought to Chiron, a centaur and the camp's director. Chiron is surprised to see Jason alive but won't give the teen any additional information about his past. Jason has a vision of Hera in which she tells him that she is his patron, which means she owns him. She repeats the message she gave to Piper about the earth's destruction if she is not released from her prison. Chiron tells him that a great threat is coming, one that has been prophesized for years, but he can't give any more details.
The following night, the three friends gather with the other demigods of Camp Half-Blood. Annabeth tells them that Chiron believes some of them will be called to complete a quest in order to free Hera. Rachel, the oracle who'd spoken with Piper, explains that the Great Prophecy has begun. It foretells of a time when the world will end unless seven demigods band together to fight against storm or fire. Jason gives a demonstration of his powers when he uses a lance to call down a lightning bolt. It is obvious that Jupiter, another name for Zeus, the lord of the sky, has previously claimed him. Rachel has another prophecy in which she alludes to Jason being the leader of the quest to save Hera. He will need two others, a child of the forge and a child of the dove, to follow him. He chooses Leo, and after she has been claimed by Aphrodite, Piper, to accompany him. Piper keeps secret the knowledge that a giant has taken her father, a famous actor, captive. The giant has threatened to kill her father if she doesn't betray her friends to the death.
Leo searches for the mechanical dragon. He manages to trap the dragon and fix its control panel. Although not perfect, the dragon is no longer a danger to others. He names the creature Festus. The dragon leads him to a cave where Leo discovers a workshop/bunker, abandoned by other demigods in 1864. It is obvious by Festus' behavior that this is where he'd been created. Leo discovers the plans for a flying ship — plans similar to a drawing he'd made when he was a child. The masthead of the ship looks similar to Festus.
Meanwhile, Jason has a dream in which Lupa, queen of the wolves, warns him that Juno (the Roman name for Hera) must be saved or a giant will return and destroy the world. In the morning, Annabeth advises him to search for Boreas, the North Wind, to ask for his help in finding Aeolus, the wind god. If Aeolus sent the ventus, then he may know where Hera is being kept. Jason also learns that he has a sister, Thalia Grace, who fights with the Hunters of Artemis.
Piper, Leo, Festus and Jason set out on the quest. They speak with Boreas, who directs them to go to Chicago to seek the woman who is controlling the winds. If they can defeat her and take the ventus captive, then they can continue on to Aeolus. On the way to Chicago, they are forced to battle with a family of Cyclopes — one-eyed giants.
They defeat the creatures and fly to Chicago. There, they discover Medea in a hidden store of enchanted items. Within Medea's fortress, they also discover Coach Hedge, who has been frozen and put in a cage. After battling her and capturing the ventus, the three seek out Aeolus. Before they can reach Aeolus, Festus is struck by lasers and wounded. Leo saves the dragon's head and puts it in his backpack. They then defeat King Midas, but Piper is turned into gold. Coach Hedge is able to revive Piper, but she suffers from hypothermia from the experience.
Jason, Piper, Leo and Coach Hedge continue on to the Rocky Mountains. As they give Piper time to heal, they encounter Lycaon, the first werewolf. Lycaon became a werewolf as a punishment for serving Zeus human flesh for dinner. Lycaon and the wolves that serve him have promised to deliver Jason to one of their friends so she can kill him. Leo, Piper and Hedge will then be food for the wolves. The friends try to defend themselves, but it is only the intervention of the Hunters of Artemis that saves them. Jason is introduced to Thalia, his sister. Thalia explains that when Jason was 2, their mother gave him to Hera. Thalia grew up believing Hera had killed Jason out of jealousy for Zeus' affair.
Thalia guides Jason and his friends to Aeolus' palace near Pike's Peak. The only way to reach the peak is to cross a fragile bridge. As Leo crosses, he begins to ponder why the god of the wind needs a bridge. Thalia explains that it's for times like this when mortals may need to meet with him. Leo gets excited, as he remembers that Hera called Jason a bridge. Leo figures that Jason will be instrumental in somehow joining two different worlds together. His excitement causes his body to overheat and start melting the bridge. Jason and Leo manage to cross, but Thalia must return to the other side. She promises to meet Jason on the solstice in order to free Hera.
Thalia tells Jason that he will remember the meeting place when the time is right. At first willing to help them in their quest, Aeolus warns the demigods that Piper's father is being held captive at Mount Diablo near San Francisco. He then receives a message from another god that tells him he must kill Jason and the others. Aeolus doesn't name her, but says that this god's orders must be obeyed. He calls his wind spirits to destroy the platform on which Jason and his friends are standing. One of Aeolus' servants, Mellie, helps them to escape before they fall to their deaths.
Piper's mother, Aphrodite, speaks to her in a dream. She helps Piper realize that the reason dead mortals, such as Medea and Midas, are alive again is because mother earth, Gaea, is waking from her sleep. If she wakes completely, she will free the giants, who will then destroy the world. Aphrodite warns that Piper will be the mediator between the two sides that Zeus has tried to keep apart. These two sides must be brought together or there will be bloodshed.
When Piper wakes up, she realizes her mother has transported her and all of her friends to California. They set off to rescue Piper's father from Enceladus, one of the giants. Piper, Jason and Leo, with a little help from Zeus, manage to trap the giant within the earth. They save Piper's father and send him back to his home. Coach Hedge offers to protect him. After basking in her father's accolades for the first time in her life, Piper gives him a potion to make him forget his ordeal. Although he'll also forget how she saved him, Piper knows her father could not live with the knowledge that gods and monsters are real.
Leo flies Jason and Piper in a helicopter to Wolf House, the ruins of Jack London's mansion in Sonoma valley. London was a demigod, the son of Hermes. The home was built on sacred ground. When they arrive, Thalia and the Hunters of Artemis are battling with various ogres, wind spirits and wolves intent on keeping Piper, Leo and Jason from finding Hera.
Jason and his friends find the queen locked up in an impenetrable cage. Before Leo and Piper can work out a way to free her, Khione — daughter of Boreas, the north wind — arrives. She has been working with Gaea to destroy Jason and his friends since the beginning of their quest. Khione believes that killing Jason and framing the Greek demigods for his death will start a war. Jason's memories are returning, and he realizes that there are two branches of demigods, Greek and Roman. The two are kept unaware of each other because of wars in the past. While Jason, Leo and Piper attack Khione and her minions, their true enemy begins to take shape — Porphyrion, the giant king.
The weaker Hera becomes within her cage, the stronger Gaea is able to make Porphyrion. Jason distracts the giant while Piper and Leo try to free Hera. They finally succeed, and Hera turns herself into pure energy in order to defeat all their enemies. Jason doesn't heed her warning to avert his eyes and so is rendered unconscious by the sight. The others, including Hera, fear he's been killed, but Piper manages to call him back from death. Hera warns them that Porphyrion isn't dead. He is hiding until he can be restored to his full strength.
Jason and his friends return to Camp Half-Blood. Leo brings the other children of Hephaestus as well as Jason, Piper and Chiron to see the bunker he found. When questioned, Chiron admits that the place has been abandoned since the civil war between the demigods, which mirrored the mortals' Civil War. Since then, the children of the Greek and Roman gods have been kept apart. The great prophecy suggests that in order to fight Porphyrion, demigods from both nations must come together. Leo is going to build the flying ship he'd first dreamed about as a youngster. Then he, Piper and Jason will travel to the original Mount Olympus to try and recruit the other demigods to fight on their side. Jason also recruits Annabeth to join the quest because he's certain that her boyfriend, Percy Jackson, has been transported to Mount Olympus.