Beyonders starts with Jason Walker, a 13 year old boy who helps work at the zoo, and also plays baseball. Jason went to the zoo as he normally does, but this day, he heard music. As he went searching for the source, he found that it seemed as if it was coming from the hippopotamus section of the zoo. Bending over to investigate, Jason accidentally falls over the railing, right into the hippo's mouth. This is when he realized he was in a different world than his own. This world is called Lyrian.

When he first arrives. he hears of a band, called the Giddy Nine, who are riding on a raft going over a raging waterfall. Jason wants to try and save them, but the rescue team refuses to help unless the musicians themselves ask for it. Jason couldn't bare to see the musicians die a pointless death, and shoved one of the rescue team members into the river, so that he may try to rescue them. Instead, she shot one of them in the shoulder with the rescue rope, and had to flee the scene without knowing who had survived or not.

Jason finds the Repository in the forest, meeting the Loremaster. The Loremaster tells him about their world, which is ruled by an evil wizard named Maldor, and about the language of Edomic, used by wizards which grants them their power. However, he tells Jason never to go to the second level, due to the forbidden information there. Jason's curiosity causes him to go the door, and he sees a lock there. With some investigation, he is able to break the lock and go onto the second level, where he finds The Book of Salzared, where he finds the 1st syllable of a word that is able to undo the wizard Maldor, but also reveals Jason's location to him. Now, Jason must leave in order to find the 5 other syllables of the word, in order to defeat Maldor.

He sets off the find the Blind King Galloran's castle where he believes he can find another syllable, or clues to find one. Once he meets Galloran, he is told there is another Beyonder, like him, named Rachel, who is about the same age. He is told that their best chance of returning to their own world is to quest for the syllables of the word for Maldor. Galloran arms them with a knife and orantium, an explosive material, and they set off to find Jugard, who knows the 4th syllable. He is said to be found in a cave near a cliff.

Once they recover the 4th syllable, Jugard tells them to go to the town of Trensicourt to find Nicholas, who may know the 3rd syllable. On the way, they meet Ferrin, a displacer, who can detach and re-attach his body parts. They only find his head at first, and help him recombine his body. Once they reach Nicholas, he tells them the syllable is inside the royal lorevault, and that another syllable is at the center of White Lake. In order to get inside the lorevault, Jason challenges the chancellor to a battle of riddles, which Jason wins and recovers the 3rd syllable.

Soon after, he receives an invitation to the Eternal Feast from Duke Conrad, who serves Maldor. They ignore the invite and go to Whitelake, who's surface is like quicksand. In order to retreive the syllable, Rachel runs lightly across the surface. On the island, she meets Malar, another displacer who only has his head and one arm He tells them the 5th syllable, and tells them that the 6th syllable is found in the Sunken Sands. He also reveals that Ferrin is Maldor's spy, so Rachel confronts him, and Ferrin leaves them to continue their journey.

On their way to the Sunken Sands, they meet Jasher, an Amar Kabal. He was sent by Galloran to help protect them. They find a giant tree where the Pythoness lives, who knows the 6th syllable. They discover that the Pythoness is dead, but her daughter Corrine tells them the 6th syllable.

The last syllable they need is the 2nd one, tattooed on Kimp, who serves Duke Conrad at the Eternal Feast. Jason must go alone to Harthenham Castle, and he finds the last syllable. However, when he asks to leave, Duke Conrad forbids him to, and challenges him to a duel to the death. Jason defeats him using billiard balls as the weapon, without killing him. Once he leaves, he is followed by Kimp and Duke Conrad's boarhounds and is attacked by them. Jason has only minor injuries, but Jasher is killed in the fight. Jason and Rachel have to separate due to chasers, but he tells her the last syllable.

Jason goes to the Felrook stronghold where Maldor is, and speaks the word, arimfexendrapuse, in his presence, but it has no effect. He then learns from Maldor the word was a trick in order to keep any heroes from directly trying to kill him, since the word is for a different, dead wizard. Jason refuses the offer Maldor makes of serving him, and is then sent to Felrook dungeons where he is tortured.

After awhile, Ferrin comes to save Jason, and takes him to a cave that is a pathway to the Beyond. Ferrin forces Jason to leave his friends and go to the Beyond, but Jason takes Ferrin's hand with him.