Percy discovers that Luke is on his own quest for revenge and plans to use the Labyrinth to enter the heart of camp to destroy it. He finds an entrance with Annabeth to the Labyrinth and descend into it so they can stop Luke and his army. Their goal is to find Daedalus, which is an extremely difficult task since the Labyrinth continuously changes and grows on its own. It causes madness, which frequently leads to death. 

The friends fight monsters, free prisoners, solve riddles, and succeed in challenges on their way to finding Daedalus. At one point, Percy becomes separated from the others after he blows up Mt. Helens. He lands on Calypso's island and has to decide whether to become immortal and live in paradise with the beautiful woman or go back to finish his quest to save the world. He makes the difficult decision and leaves. 

Even though it's Annabeth's quest, the answer to getting through the Labyrinth lies in Percy. He realizes that they have to enlist the help of a mortal named Rachel. She has the unique ability to see through the Mist. While others struggle to choose between paths in the Labyrinth, she can see the correct route clearly. They eventually reach Daedalus, but he is hesitant to help them.

Grover is on his own quest. He has to find Pan and prove his existence or he will lose his job. While in the Labyrinth, the friends find Pan who is about to cease his existence. He breathes part of himself into each of the members present in the room, except for Nico, who is the son of Hades. 

Luke finds Adriane's string, which leads his army out of the Labyrinth into Camp Half-Blood. A fierce battle ensues. Grover bellows, and the sound scares the enemy away. This sound came from the part of Pan that now lived within him. When the battle is over, Daedalus lets himself die, therefore closing down the Labyrinth forever.