The hero of Illusion of Gaia, this school-aged boy returned to South Cape one year earlier without his father, who was lost during a voyage to explore the biblical Tower of Babel. Will is determined to find his father again, though he seems a bit fuzzy on what exactly happened. Since the return, he has discovered he has a limited psychic ability, and at the outset of the game finds that he is able to see (and enter) portals to another dimension called "Dark Space." He has a close relationship with his friends and relies on them for advice, companionship, and aid on his journey; yet Will, as he will come to learn, is perhaps the only one with the power to save Earth from the approach of chaos from the sky. He learns to persevere in his calling, even as others must sacrifice to help him.
A selfish, spoiled princess of nearby Edward Castle (Edward being her father), Kara encounters Will while leaving the castle on one of her semi-regular rebellions against the stifling restraints of her life. She visits South Cape and meets Will and his grandparents before being dragged away by guards. When Will is beckoned to the castle to surrender his father's ring, she pleads for his aid in helping her escape, and when his audience goes badly, she sends her loyal pig Hamlet to release him, joining him afterwords. Kara grows more than any other character in the story, transformed by her experiences from a sulking, obstinate brat to a confident, useful contributor and Will's closest friend. As the game approaches its end, Kara reaches a potential far beyond her shallow beginnings.
One of Will's three school friends, Seth comes from a hostile home, and prefers to spend most of his time playing cards with his companions at their secret seaside cave. Intelligent and adventurous, Seth is a normal school boy of his age. He has the best diagnosis of Will's budding powers when Will demonstrates them, and comes with the other boys to join Will on his quest. Unfortunately for Seth, a strange and terrifying fate awaits him in his journey, but one that will later help Will to understand what his quest encompasses and why it is important.
Another of Will's school friends, Erik's family is the oldest of South Cape, and their house is the biggest. This doesn't seem to rub off on Erik, though, who is Will's most affable companion, never presenting Will with difficulties and always helping with advice. Erik seems to reflect Will's former life as a normal boy, as he follows Will throughout the entire game but undergoes no particular character change from his carefree days hanging out in the cave, except in adapting to the rigors of the traveling life. Erik is a source of scatological humor, constantly being interrupted in his attempts to go to the bathroom.
A close friend of Will, Lance also lost his explorer father in an expedition. His only remaining family is his mother, who knew Will's family. Lance is the most forthright of the group, stating his mind and pushing the others to a course of action. While not quite bossy, he's definitely comfortable putting his foot down on a course of action. Being a loyal friend, this course of action is usually to follow Will; that is, his time with one of his traveling companions bring him to find love.
An adolescent child from Itory Village, Lilly is protected by the Flower Spirit and can transform herself into a dandelion and fly through the air at will. While just as headstrong as Kara, Lilly is her polar opposite in experience, knowing much of nearby world from her travels, and has little patience for her. She is proud of the unique nature of her magical village and people and knows Will's family through his mother's side. She is assigned by her tribe to help Will escape from Edward Castle, but discovers her aid is unnecessary. She is an energetic, hard-working companion who wants to help Will succeed, but eventually she finds something more in another member of the group.
Will's long-lost cousin, Neil is modeled as a Leonardo DaVinci of the world, inventing such myriad devices as the telescope, the camera, and the airplane. When their journey deposits the group relatively near his workshop, Will decides to take a detour to ask Neil for advice for how to accomplish the mysterious task he's been given. Neil is an eccentric but kind man, willing to help with the interesting challenges facing Will. An incident leading to an attack of conscience will bring Neil to leave his tinkering and adventuring behind and become respectable.
Kara's pet pig, Hamlet, displays an empathy beyond what most would expect from a farm animal. Willing to brave a dungeon, the world, and even death to help his mistress and other human beings in need, Hamlet represents a pure goodness and the duty of friendship in his brief time in the story.
A bounty hunter relentlessly pursuing Kara as per her parents' orders. Though only encountered once late in the game, there are often hints suggesting he is on Will's tail.
An enigmatic "Dark Knight" whose body Will inhabits during many dungeon sections, due to his superior martial ability. Freedan also has several powers that are required to progress in dungeons.
An even more mysterious character, Shadow is able to merge with the floor and walls to reach new areas. He is unlocked for Will's use close to the end of the game.
Will's main benefactor, Gaia is a goddess that represents the Earth who resides in the Dark Space, giving the player hints on where to go next. Her counterpart is the Dark Gaia, a comet currently heading towards the planet. Dark Gaia is responsible for many of the ills in the world.