A coast guard boat picks Percy, Annabeth, and Grover up in the middle of the bay, where the bubbles had carried them up from the Underworld. Percy and Annabeth both have put two and two together and realized the trick, but Grover still cannot figure it out, so Percy explains. "The god who has turned" from the prophecy was not Hades, but Ares. Ares wanted war so badly that he stole the master bolt and Hades's helm and framed Percy. Sure enough, Ares is there waiting for them at the shore on his motorcycle. Percy accuses him, and he says he did not steal the bolt personally, but does not reveal whom he used. He pulls Hades's helm from his pocket and shows it off.
Ares will not explain why he sent the master bolt to Hades in the Underworld with Percy in the first place; Percy guesses that it was actually the being in the pit that ordered the theft, and Ares is answering to that creature. Ares denies it, but is clearly uncomfortable. He says he has to kill Percy to prevent him from bringing the bolt to Olympus, and summons a wild boar monster. Percy calls up a wave to swallow up the boar, and then challenges Ares to a duel. Annabeth gives Percy her necklace of camp beads for good luck, calling it a reconciliation of Athena and Poseidon together. Grover gives him a flattened tin can as a token of the satyrs' support.
Each armed with a sword, they fight back and forth for a while, and Percy uses the water to his advantage. Ares tries to keep Percy out of the water, and Percy struggles against him. Suddenly cops show up, but Percy's ADHD battle senses keep him focused and noticing every detail. The cops tell them to drop the guns, which is how they are seeing the weapons, but Ares sends a wall of fire at them and explodes their cars. In one last effort, Percy drops his blade and feigns exhaustion, then calls up a wall of water to smash Ares in the face.
Percy takes that moment to stab Ares in the heel, and Ares, bleeding ichor (the golden blood of the gods), is stunned that Percy managed to injure him. He limps toward Percy to attack him, but a strange force stops him, and a cold, heavy presence passes over the beach for a moment before lifting. This stops Ares, and he warns Percy that he has made an enemy of him, and then assumes his true immortal form. Percy and the others turn away from his blinding brightness as he disappears. The Mrs. Dodds Fury appears, having watched the entire altercation. She concedes that Percy was not the thief, and Percy gives her the Helm of Darkness to return to Hades so that he will call off the war.
The only way they will make it to New York before the summer solstice deadline is by flying, after the news media clears Percy's name and says that all his efforts had been meant to get away from the large man on a motorcycle who had kidnapped him. When the trio gets to New York, Annabeth and Grover head straight back to Half-Blood Hill to tell Chiron what happened, and Percy heads into Manhattan. He goes up to the 600th floor of the Empire State Building in the elevator, and comes out far above Manhattan at the base of a floating mountain peak in the clouds. A city of dazzling white classical buildings winds up the mountaintop, and Percy makes his way to the palace at the peak.
He enters the throne room with thrones for each of the twelve Olympians. The gods are in their human form, with Zeus in the middle wearing a pinstriped suit. Next to him is Poseidon, wearing Bermuda shorts and a Tommy Bahama shirt. Percy is in awe of the sight of his father, and kneels at his feet. It seems that Poseidon does not know what to think of Percy, and does not show outward warmth, but Percy is fine with this because it means he is not trying to fake affection. Percy then addresses Zeus and tells him his story, laying the master bolt at his feet.
Neither god can believe Ares would do such a thing, but Percy tells him he did not act alone. He explains about his dreams and about the powerful creature in the pit that felt older than even the gods. Zeus grudgingly thanks Percy for his work and disappears, leaving Percy with his father. Poseidon explains that in the pit is Kronos, king of the Titans and Poseidon and Zeus's father, and tells the story of how Zeus cut Kronos into a thousand pieces and banished him to the pit of Tartarus. Percy insists that Kronos intends to rise from the pit and come back to power. Poseidon then tells Percy he must go, but reveals that his mother has been returned, since he returned the helm to Hades. As Percy leaves, Poseidon tells him that he will soon have to make an important choice, and that he is proud of him.
Percy goes home to his apartment, where his mother has reappeared. Gabe is worse than ever and picks a fight with Percy, and his mother still attempts to defend Gabe and insist he is not all bad. On his bed, Percy finds the packaged head of Medusa that he had tried to send to Olympus, and realizes that the gods gave it to him so he can get rid of Gabe by turning him to stone. Percy leaves the package with his mother, so that she can decide whether or not to use it on Gabe if he continues to threaten her. Percy heads back to Half-Blood Hill.
Everyone is thrilled that Percy, Annabeth, and Grover have retuned to Camp Half-Blood alive. Grover is granted his searcher's license at last. Percy is happy, thinking of his father being proud of him and his mother's chance at a new life, since it seems she decided to turn Gabe to stone after all and sell him as a prized stone sculpture. She put down a deposit at NYU and moved into a new apartment. She says in a letter that if Percy wants to come home for seventh grade, there is a school for him in the city. Percy is still not sure if he will go home or stay at camp year-round.
Grover heads off on his searcher's quest, and the camp votes to have a bead with a trident on it represent that summer in honor of Percy's quest. Everyone packs up for the year, and Percy still cannot decide whether to stay or go home and live with his mother. He spends the last day of the summer training, and runs into Luke, who asks him to take a walk. Luke reveals that he is leaving Camp Half-Blood and summons a pit scorpion to kill Percy; Percy realizes that Luke is the friend in the prophecy who will betray him. Luke reveals that he serves Kronos and that he was the one who stole the bolt and the helm on the winter solstice and convinced Ares that all this was worth the war it would cause. The flying shoes were meant to carry Percy to Tartarus with the bolt for Kronos, but he gave them to Grover instead.
Luke disappears, off to serve Kronos, and Percy fights off the scorpion, killing it, but not before it stings him. He blacks out as nymphs take him back up to camp, and then comes to in the sickroom of the camp's Big House, with Annabeth next to him feeding him nectar. Chiron was able to heal him. Percy tells Chiron and Annabeth what happened with Luke, and is determined to go out right away and track down Luke. Chiron tells him that now is not the time, but that his time will come. Annabeth tells Percy that she is going home for the year to try and live with her dad again, and they agree to hunt down Luke next summer. As the novel ends, Percy makes the decision to do the same.
These final chapters overturn everything Percy and his friends thought they knew and show him that he misinterpreted the prophecy. Percy traveled all the way on a hunch; everyone assumed that Hades had stolen the bolt, but no one actually knew for sure that it was him. It would be easy for Percy to feel demoralized and like he had come all this way for nothing, but Percy needed to make this journey both to learn the truth and to grow as a hero and as a person. He has learned the importance of friendship and the precariousness of trust, and has come to terms with many of his own abilities.
While Percy may have been called a "hero" as soon as he learned he was a half-blood, he does not truly earn this title until he finishes his quest. He has made many heroic decisions along the way, and his heroism is rewarded when he travels to Olympus and is greeted with a hero's welcome upon passing through the city. Though he is young, Percy has achieved a status equal to heroes of old mythology—Hercules, Theseus, and his namesake, Perseus, alike. He is gracious enough, however, to acknowledge that he did not do it alone, and would not have succeeded without the help of his friends.
For the first time, Percy interacts with his father. Percy's two parents are juxtaposed in these last chapters: his mother, warm and loving, directly contrasts his father, who is reserved and stern with his son. This interaction shows that neither Percy nor Poseidon knows how to handle the presence of the other, since they have only dealt with each other from afar. However, when Poseidon tells Percy he is proud of him, Poseidon feels the sort of kinship with him that a son should feel for his father, indicating great potential for the relationship between Percy and the sea god.
Percy's cleverness, strength, and wise decision-making over the course of his quest means he is rewarded with what he wanted most: his mother back from Hades's clutches. But his mother gains just as much from Percy's victory as he does. She has spent Percy's entire life trying to protect him, living only for him without thinking of herself. Now that Percy has acquired agency and knowledge of his heroic parentage, this selfless woman has room, for the first time, to think about herself. Sally Jackson's willingness to take control of her own life, get rid of Gabe, and begin on a new path shows a kind of resilience and strength that she clearly passed on to her son.
While this particular quest is resolved, it is clear that Percy has not seen the end of the conflict yet. Riordan chooses to end the first book in the series with Luke's betrayal, leaving readers as outraged as Percy is and paving the way for a future quest to stop Luke and Kronos. This betrayal hits Percy hard, since throughout this book, he has placed great trust in his friends and shown how much he values their companionship. Even though Luke was not on Percy's quest, Percy still considered him a friend, and it affects him deeply to see a bond like that break. But Percy does not allow this betrayal to defeat him; instead, he keeps his head up and focuses on the future.
At the end of the novel, both Annabeth and Percy make the choice to go home and spend the year with their mortal families. This shows that both of them have come to terms with their double identities. Part of being a demigod is embracing mortal lineage as well as divine, and if Percy and Annabeth were to continue to ignore their past and remain living at camp for the year, they would turn their backs on that essential part of their lives entirely. In the mortal world, they will be tested rather than sheltered the way they are at camp, and they recognize that they will only become stronger because of it.