The Lightning Thief is narrated in the first person past tense by Percy Jackson, a twelve-year-old diagnosed with dyslexia and ADHD. On a school trip to the Metropolitan Museum of Art, one of the chaperones, Mrs. Dodds, turns into a Fury and attacks him. The other and Percy's favourite teacher, Mr. Brunner, lends Percy a magical sword-pen to defeat her. After school lets out, Percy then goes on a trip to Long Island with his mother, Sally. In the middle of the first night, Percy's friend Grover Underwood, who is reveals himself to be a satyr, tells them they are in danger and the three drive to a mysterious summer camp. The Minotaur attacks them, grabs Mrs. Jackson, and causes her to disappear in a blinding flash of gold light. Believing his mother has died, Percy in a rage kills the beast with one of its own horns, then drags the unconscious Grover into the camp, soon falling unconscious himself. Percy wakes up three days later and learns that the camp is called Camp Half-Blood and that he is a demigod: the son of a human and a Greek god. He settles into camp life and meets several other demigods, including Luke Castellan and Annabeth Chase. After a hellhound attacks him after a game of Capture the Flag, he is saved by Chiron and then claimed by his father, the god Poseidon. Chiron explains to Percy how the three eldest male gods—Poseidon, Zeus, and Hades—swore an oath not to have children more than 70 years ago; Percy represents a violation of the oath that was made. This, coupled with the fact that Zeus's master lightning bolt has recently been stolen, has bred much suspicion and discrepancy between the gods.
Percy is given the quest of locating Zeus's original lighting bolt before an all-out war can break out between the gods. He chooses Annabeth and Grover to accompany him on a quest to the realm of Hades, as he is the most likely culprit of the theft. Before he leaves, Percy is given Chiron's magic sword Anaklusmos ("Riptide") and Luke's flying sneakers. The trio then travels towards Los Angeles, where the entrance to Hades's realm resides. Along the way, they are attacked by several monsters, including the Furies, Medusa, Echidna and the Chimera. They also do a favour for the god Ares, who gives them a backpack full of supplies and safe transportation to Nevada. Percy gradually learns more about his companions, his powers, and the world of the Greek gods. When they arrive in Hades's realm, Grover is nearly dragged into Tartarus by Luke's flying shoes. The battered group finally meet Hades, who reveals that his Helm of Darkness has also been mysteriously stolen. Hades accuses Percy of stealing his helm and threatens to kill Sally Jackson (who has been held hostage by the god) and reanimate the dead unless his helm is returned. When Percy finds the missing master bolt inside Ares's backpack, the group realizes they've all been manipulated by Ares. Narrowly escaping the Underworld, Percy challenges Ares to a duel on the beach. After a long and tough fight the demigod wins, gives the Helm of Darkness to the Furies; Hades then realizes that Percy was not the thief of his helm nor the master bolt, he returns Mrs Jackson to their apartment in New York.
Percy takes the master bolt back to Zeus on Mount Olympus, who rewards the young hero by not killing him as his laws recommend. Percy returns to camp half-blood a hero and enjoys the rest of his summer there. On the last day of camp, however, he goes into the woods with Luke, who reveals himself to be the real thief of the Hades's Helm and Zeus's bolt, following the orders of Kronos. Kronos also manipulated the power-hungry Ares into taking part in the scheme. Percy can't believe that Luke would do that, and so Luke explains his beliefs that the gods are too irresponsible and are poor leaders who need to be overthrown. He offers Percy the chance to join him, and when Percy refuses Luke tries to kill him with a scorpion. Percy manages to kill it, but is badly poisoned and faints. When he has awakened and recovered, Percy is given the choice of whether to return home for the school year or stay at camp year round. After much thought, he decides to spend the school year with his mother (who is no longer with his alcoholic, smelly stepfather Gabe since he got petrified by Medusa's head), even though it will be more dangerous for him with Luke and Kronos on the loose. Grover and Annabeth also leave the camp for the year, but promise to keep in touch with Percy.