Magi Nation follows Tony Jones, a timid human teenage boy, who has just recently moved into a new town.

He is escorted to the city of Vash Naroom, located in a network of tree canopies and constructed of wood.

In the following events, Tony is mistaken for a prophesied hero named "Magus Kyros" and, with no other option, he ventures across this new world, searching for the means by which he can return home.

Tony travels to an area west of the Naroom Forest known as the Weave, and finds the home of Gia, the wise old woman whom Eidon trains under.

This event leads her to believe that Tony may be the legendary Magus Kyros, who was prophesied to return to Magi Nation in a time of great peril.

Outside of town lies Gruk's mushfarm, where Tony ventures to help her resolve the strange noises coming from her basement.

Tony arrives and is unable to save her from being kidnapped by Zet and Korg, who later make ridiculous demands to the Underneath townspeople in exchange for Gruk.

Motash realizes that Tony is the great Magus Kyros, and implores him to destroy the Geyser and then leave the Underneath.

After waking up from his faint in Wence's house, Tony returns to Gia's hut and tells her the terrible news about the Underneath.

After stealing the key to the vault from Ashgar's house, Tony travels aboard a ferry to the island of Orothe.

Unable to swim, but desperate, Tony blows the horn Blu had given to him earlier and dives off of the edge of the fortress.

Blu conveniently arrives and gives Tony a belt that allows him to swim and breath underwater, before leading him to Orothe, which is actually an undersea city resting on giant turtles.

Tony learns that a Shadow Geyser has appeared in Orothe, and all attempts to enter it have failed due to a barrier.

Tony searches nearby ruins and learns a new spell that allows him to disable the barrier and enter the Shadow Geyser as the remaining Orotheans leave the area.

Gia explains that Tony is not the Great Magus Kyros, and that his mere presence in the realm has allowed an ancient enemy of the Magi, Agram, to return.

Tony heads back to the Core, seeing hundreds of petrified people, including those he has met along his journey, along the way.

It is optional to refuse to step into the light by trying to leave the throne room, in which case Tony can attend the funeral (or party).