The story begins when the Magic Tree in Yan's home village of Corris starts to die. This Magic Tree (the Tree of Life) is one of five which has ensured peace and harmony to the people and creatures of the world of Lorth - where the adventure takes place. What follows is an epic adventure through many different environments, featuring a variety of characters, equipment and abilities.

Yan, the main protagonist, is a 19 year old man, who was raised by the Magic Tree's sentinel after being found lying in a bundle of blankets next to the Tree of Life. The Sentinel took the young baby into his home and raised him as his own child, along with his son Gareth.

The Roots features an epic storyline with the forces of good and evil battling for control over the world. The gamer is caught up in the middle of this eternal conflict and plays a pivotal part in the destiny of his homeland. Through his journey, the player will encounter many different characters. The Roots has over 100 non-playing characters - many of them will have their own agendas, which might not be apparent straight away and could conflict with the gamer' s mission.