Several years ago, on the island of Ilusia, a great disaster took place at the base of the Mana tree and many lives were lost, leaving the main characters as orphans. A brave young boy and girl used the Sword of Mana to save the world from disaster. Now, years later, the main characters set out to investigate the details of the event that took so many loved ones away from them. The four major characters of Children of Mana are Ferrik, Tamber, Poppen, and Wanderer. They all live together in the Mana Village, near the Mana Tree. One day the stone at the base of the Mana Tree cracks following a flash of light, distorting time and space. Ferrik (if that is the character the player chooses to play with) recalls how his friend Tess, who is a priestess, went to the Mana Tower to pray. After reaching the tower with an Elemental in tow, Ferrik finds the tower is infested with monsters. Upon fighting his way to the top of the tower, Ferrik finds Tess, frightened but unharmed. Suddenly, a giant flaming bird descends upon the two. Ferrik attempts to fight it, but finds that the bird is protected by a sort of barrier.
Then, out of the blue, a tall sword falls from the sky. The sword's power causes the bird's shield to fade away, allowing Ferrik to slay the beast. When the bird is defeated, a mysterious man garbed in black appears. He attempts to take the Holy Sword, which is still stuck in the ground, but finds that it is protected by a barrier. Intruiged, the man disappears, upon which Ferrik takes the Holy Sword, which turns out to be the fabled Sword of Mana.
Upon returning from the Mana Tower, Ferrik discovers that three mysterious pillars of light have struck in the lands of Topple, Jadd, and Lorimar. Ferrik after being asked by Mayor Moti and Watts the Dwarf, investigates these places in each one finding a huge monster at the end. After completing his task in Lorimar, the mysterious man appears once again, identifying himself as the Mana Lord. He steals the Mana Sword and brews up a large storm in the land of Wendel. Ferrik must once again head out to a distant land and stop the Mana Storm. There is once again a confrontation with the Mana Lord. When he is about to kill Ferrik, a group of gems appear around him to prevent his attack. He decides he must kidnap Tess and vanishes. Ferrik races back to the Mana Village.
From there Ferrik heads to the Ruins, which turns out to be what Illusia will be like if things keep going the way they are going. After defeating the shadows of his former family in an epic boss battle, Ferrik finds nothing but a little toy horse, which he keeps.
Following the adventure in the Ruins, Ferrik heads for the Path of Life under the roots of the Mana Tree. At first the entrance seems to be sealed, but the toy horse Ferrik found in the Ruins conveniently opens the way.
At the end of the Path, the Mana Lord is waiting for Ferrik. Upon his defeat, the Mana Lord reveals that he never intended to directly harm anyone, that he was one of the two children of Mana, the other spreading disaster through the world, and that he was simply trying to fulfill the reason he was created: "to fill the world with the power of Mana." He then proceeds to give the Mana Sword to Ferrik, then throws himself off a cliff in an act of suicide. This shift in power causes a rift to open in the sky, where the second child of Mana waiting. Ferrik destroys this second child, restoring the world to peace.
In the aftermath, Tess and the Elementals are entrusted with care of Illusia, while everyone else must leave. Moti says that Illusia will be protected as a haven, and that humans won't return for many more years. They make for Jadd, to start a new life in a new world.