The story is set in an alternate recreation of the ancient Old World with several regions and nations having some resemblances with real-life counterparts from that time. In this world, all living beings possess an essence known as Rukh and when they die, this essence returns to the huge flow (also known as "guidance") of Rukh that gives life to all subsequent beings in an eternal cycle of rebirth called "Fate". Once a person is overcome with sadness, anger, and hopelessness, their Rukh becomes corrupted, unstable, and black, and deviates from the main guidance in a process known as "Fall into Depravity".

There are also several magic castles full of treasures and traps known as "Dungeons", which are each the lair of a powerful magic being, a Djinn. Individuals that manage to overcome the trials of a Dungeon and earn the allegiance of its Djinn are known as Dungeon Capturers, gaining the ability to use its powers infused in a personal item of theirs known as a "Metal Vessel" and create less potent "Household Vessels" for their companions as well.

People can use the Rukh in their bodies to create an energy known as Magoi to power their magical weapons and abilities. Among those that can perform magic with their own Magoi there is a rare class of magicians known as Magi, that can also use Magoi from the Rukh around them, greatly increasing their capabilities. A Magi usually chooses Dungeon Capturers to offer guidance and protection making them into their King Vessels.

Main Story:

Fourteen years ago, a structure appeared from the sea, turning into a gigantic tower. Thousands of people entered, and did not come out. Until one day, it gets conquered by two special people, a "Magi" and a "King".

Magi centers around Alibaba Saluja (a young man aiming to capture the nearby dungeon, Amon) and you (a traveler with a Djinn named Ugo in your flute).