So the Twelve Olympians have moved their home in Olympus to the 600th floor of the Empire State Building. They sire children with mortals - that is, until the Great Prophecy, spoken by the Oracle of Delphi that says that a half-blood child of the Big Three (Zeus, Poseidon, and Hades) will make a decision that will either save or destroy Olympus. Due to this, the three agree to never sire any more half-blood children. But then Zeus, who ironically has the idea of the oath, fathers a girl named Thalia Grace. Hades is enraged by Zeus breaking his own oath and sends his fiercest monsters from the Underworld to hunt Thalia down.

While running away, Thalia meets two half-bloods: Luke Castellan, a son of Hermes; and Annabeth Chase; a daughter of Athena. The three decide to team up and become some sort of family to one another. Eventually, the three make it to Camp Half-Blood, a sort of sanctuary for half-bloods. However, the monsters catch up to Thalia and mortally wound her - but before she can die, Zeus turns her into a tree to save her. This enrages Luke, and it’s made even worse three years later when his quest to the Garden of Hesperides results in him being scarred. Eventually, Luke is visited in his dreams by Kronos, King of the Titans. Kronos convinces Luke to steal Zeus’ master bolt and Hades’ helm of darkness. Zeus sends his sons and daughters to catch the thief, and eventually, Ares catches Luke. However, Kronos, through Luke, tells Ares that the loss of the two items would result in a war, intriguing him.

Hades, on the other hand, sends his Furies out to look for who stole his helm. One Fury, while posing as an algebra teacher named Mrs. Dodds, discovers a half-blood in the form of Percy Jackson, a 12-year-old boy with dyslexia and ADHD like every other half-blood, while on a field trip to the Metropolitan Museum of Art. She reveals her true form to Percy and attacks him. Percy's favorite teacher, Mr. Brunner, later revealed as Chiron, lends Percy a magical sword-pen to defeat her. After the school year ends, Percy's mother, Sally, takes him to Long Island. Percy's friend from school, Grover, reveals himself as a satyr and warns of danger, advising Sally to take Percy to a Camp Half-Blood. On the way, the Minotaur attacks the group, causing Sally to disappear in a flash of light. Percy kills the beast with one of its horns.

At camp, Percy learns of his identity as a half-blood, settling into camp life and meeting several other demigods, including Luke and Annabeth. After a hellhound attacks him during a game of Capture the Flag, he is saved by Chiron and then claimed by his father, the god Poseidon. Chiron explains to Percy about the Big Three’s oath; Percy's birth was a violation of the oath.

Percy is sent on a quest to locate Zeus's Master Bolt. Annabeth and Grover accompany him to the realm of Hades, who is believed to be the most likely culprit. Percy brings with him Chiron's magic sword, Anaklusmos, and Luke's flying sneakers. The trio travels to Los Angeles to visit Hades. Along the way, they are attacked by the Furies, Medusa, Echidna, and the Chimera. They perform a favor for the god Ares (finding his shield at the tunnel of love), who gives them a backpack full of supplies and safe transportation to Nevada, where they are stalled by the Lotus-eaters. In Hades's realm, Grover is nearly dragged into Tartarus by Luke's flying shoes. The battered group finally meets Hades, who reveals that his Helm of Darkness has also been mysteriously stolen and accuses Percy of stealing it. Hades threatens to kill Percy's mother, Sally, and unleash a zombie apocalypse unless his Helm is returned. When Percy finds the missing Master Bolt inside Ares's backpack, the group realizes Ares has manipulated them. After they narrowly escape the Underworld, Percy meets Ares again on the beach and challenges him to a duel. After an arduous fight, Percy wins, and he gives the Helm of Darkness to the Furies. Hades realizes that Percy is not the thief of the Helm nor the Master Bolt and returns Sally home.

Percy takes the Master Bolt back to Zeus on Mount Olympus and meets his father, Poseidon. Percy returns to Camp Half-Blood as a hero and enjoys the rest of his summer. On the last day of camp, he enters the woods with Luke, who reveals himself as the real thief of Hades's Helm and Zeus's Bolt, following Kronos's orders. Kronos had also manipulated the power-hungry Ares into participating in the scheme. Luke explains that the gods are irresponsible, poor leaders who should be overthrown. He offers Percy the chance to join him, and when Percy refuses, Luke tries to kill him with a scorpion. Percy is stung and faints. When Percy wakes up, he is given the choice of staying in camp or going home for the school year. He decides to spend the school year with his mother. Grover and Annabeth also leave the camp, with Grover leaving to find Pan and Annabeth leaving for a family reunion.

One year later, Percy wakes up on the last day of his peaceful seventh-grade year at Meriwether College Prep after a dream about Grover being in danger. He has befriended Tyson, a homeless child the school has taken on as a form of charity. In gym class, while playing dodgeball, Percy is attacked by Laestrygonians but is saved by Tyson and Annabeth, who was returning to Camp Half-Blood after having dreams about the camp in danger.

The three take a magical taxi driven by the Graeae to camp. There, they see campers led by Clarisse LaRue battling Colchis bulls. Tyson is granted permission to move past the camp's boundary to save Percy again, revealing that he is a baby Cyclops and Percy's half-brother, as he is also a son of Poseidon.

Someone has weakened the protective walls of Camp Half-Blood by poisoning the tree of the demigod Thalia, leaving the campers vulnerable to future monster attacks. Camp counselor Chiron is accused of poisoning the tree and is fired. Before leaving, Chiron notes that only the Golden Fleece can save the camp.

Due to his charm and skill with a sword, Tantalus becomes the new camp counselor. As a reward for winning a chariot race, Tantalus sends Clarisse LaRue to find the Golden Fleece and forbids anyone else from leaving camp without his permission. After talking with the god Hermes about the fate of his son Luke, Percy leaves camp with Annabeth and Tyson to find Grover. Aided by a hippocampus named Rainbow, the trio reach the Princess Andromeda, a cruise ship filled with monsters and demigods that allied with the titan Kronos. On board the vessel, they are captured by Luke, who is working to revive Kronos. The trio escapes on an emergency lifeboat and takes shelter in a hideout that Annabeth, Thalia, and Luke built as children. A hydra attacks them there, but Clarisse saves them on her ship, the CSS Birmingham.

Annabeth, Percy, and Tyson join Clarisse's quest to the Bermuda Triangle. To enter the Triangle, the ship tries to pass between Charybdis and Scylla, who attack and destroy it. Clarisse gets separated from the others while Tyson seemingly dies in the explosion, so Percy and Annabeth board a lifeboat and head to the nearest island. After traveling through the narrow strait that Charybdis and Scylla guarded, the two land on the island of the witch-queen Circe. Realizing that she has turned dozens of men into guinea pigs, they turn the guinea pigs back into men and escape on the pirate's ship Queen Anne's Revenge, which Percy can control.

The duo manage to pass the Sirens and reach the island of the cyclops Polyphemus, discovering that he has captured Clarisse. Before journeying to the island's center, Percy and Annabeth meet Grover, pretending to be a female cyclops to trick Polyphemus into not eating him. Tyson also arrives to help, having been rescued by Rainbow from the Birmingham's wreckage. They find the Golden Fleece, but Polyphemus destroys the Queen Anne's Revenge, forcing the group to escape on Rainbow and a few