The novel opens with Percy Jackson on a drive with Rachel Dare. He is approached by Charles Beckendorf, and the two head off to attack The Princess Andromeda. Kronos, hosted in the mortal body of Luke, is not caught off guard because of a spy at Camp Half-Blood, and Beckendorf is killed. Percy awakens later in his father's underwater palace, which is under siege by the Titan Oceanus. Percy wants to stay and help fight with his father, but Poseidon sends Percy back to Camp Half-Blood to hear the "Great Prophecy". Once there, Percy informs the camp of the spy and also learns the Olympians are occupied fighting Typhon. That night, Percy leaves again with Nico di Angelo, son of Hades, following a lead on how to defeat Kronos. After visiting Luke's mother in Westport, Connecticut, and talking with Hestia, Percy procures a blessing from his mother. He then descends into the underworld to bathe in the River Styx and take on the curse of Achilles. Despite being betrayed by Nico in exchange for information on the boy's mother, Percy is successful and uses his new invulnerability to defeat a small army of Hades's minions.

Percy emerges from the Underworld in New York City, leaving Nico behind to convince his father to join the fight against Kronos. Percy calls the campers to help defend Olympus, as the gods refuse to end their struggle with Typhon. Just before the battle begins, New York City is affected by a powerful sleeping spell from Morpheus, Hecate, and Kronos himself. Despite being joined by Thalia's Hunters of Artemis, the Party Ponies, and a few other allies; the Olympian army struggles to hold back repeated assaults by the Titan army. Camp Half Blood suffers approximately 16 casualties, out of an original 40 campers. Annabeth herself is badly injured when she saves Percy from an attack by Ethan Nakamura that would have hit Percy in his Achilles point. Even after these setbacks, Percy still refuses a chance to surrender offered by Prometheus, and entrusts the titan's gift of Pandora's pithos to Hestia. The campers successfully defeat Hyperion, and Kronos becomes even more enraged.

Rachel Dare, who has been experiencing inexplicable moments of prophecy, arrives to warn Percy of a deadly drakon that can only be killed by a child of Ares and that he is "not the hero". The campers do poorly against the enemy until Silena Beauregard arrives disguised as Ares's head counselor Clarisse and breaks the cabin's boycott of the war. The real Clarisse arrives in a fury and kills the drakon by herself. As Silena lies dying, the campers learn that she was the camp's spy, but chose to right her wrongs after her boyfriend Beckendorf's death.

Percy contacts his father and explains to Poseidon that Kronos is playing on their divisions; he reluctantly agrees. Driven back to the blocks surrounding the Empire State building, Percy and his friends make their last stand to protect Mount Olympus. Even when Hades arrives with Nico and an army, Kronos still manages to enter Olympus. Percy attacks Kronos, without either side gaining a significant advantage. In an Iris message-vision, the combatants are able to see Typhon approaching New York, only to be defeated with the aid of Poseidon and his cyclopes. Ethan Nakamura also rebels against Kronos's expectations, but is killed. When Kronos attacks Annabeth, Luke is able to regain control of his body and, with Percy's help, he injures himself at his mortal point and successfully banishes Kronos to the void. As he dies, Luke tells Percy that Ethan had the right idea: it was unclaimed children and unrecognized gods that really brought this war upon them. He dies peacefully, and the Fates themselves carry his body away.

The gods grant rewards to several heroes who were instrumental in defeating the Titans, including Thalia, Grover, Annabeth, Tyson, Clarisse, and Nico. Finally, Percy is called forward. Zeus offers him the greatest gift of all time: immortal godhood. Much to the Olympians' shock, Percy instead asks the gods to swear on the River Styx that they will claim all demigods by the time they turn thirteen; have cabins and thrones built for all the minor gods and Hades; and give amnesty to innocent Titans and their former allies. Percy also relieves Zeus, Poseidon, and Hades of their oath to not have demigod children. After the meeting, Percy discovers Rachel plans to become the new Oracle, he rushes to camp with Annabeth and Nico. He fears that a curse placed on the Oracle's spirit by Hades (in revenge for Zeus's murder of Nico's mother) is still in place. With Apollo's supervision, Rachel safely becomes the new Oracle and speaks the next Great Prophecy:

The novel ends shortly after Annabeth celebrates Percy's birthday and the two begin dating. The gods are keeping to their new promises, and Camp Half-Blood is slowly returning to normal. The many fallen demigods are honored with the end-of-summer's bead.