The game is a Dungeon Crawler, unlike most games in its series. The player must travel to selected areas, by traveling on Flammie, a flying mythical dragon.
To beat the place the player is in, he or she must defeat the boss, after getting through all the dungeons. To get to other floors, the player must find the Gleam Drop, and use it when on top of the Gleam Well. After the place is finished, players can enter again.
Attacking is done by pressing the A button, although when the player defeats the first boss, They are able to attack with the X button, making dual weapons possible. The player can change weapons at anytime using the R button.
The story starts out with whatever character the player picked. A cutscene is then shown explaining that a young boy and girl saved the world with the Sword of Mana. The Mana Tree then cracks and displays strange lights, distorting time and space. The main character then remembers Tess, the players best friend,
remembers that she went to the Mana Tower to pray. After selecting an Elemental Spirit to aid the player, he/she finds out the place is filled with monsters. At the top of the tower, the player finds Tess, unharmed but frightened.
A flaming bird then descends down. The player tries to fight it, after a couple of blows, the player finds out that the bird is protected by some sort of force. A cutscene then shows the Holy Sword falling down to the earth, and landing in the ground. The birds force is then shattered.
Fighting this bird again, it is then defeated, and is no more. A strange man in almost everything black appears. The man doesn't introduce himself. He goes to the Holy Sword, which is still stuck into the ground, but finds out it is protected with a barrier. Intruged, the man leaves, and the player picks up the sword (Which turns out to be the fabled Sword of Mana) and gets out of the tower. However, a strange ray of light, which poors down onto 3 lands, stops them for a second to look at what is happening.
Moti, the mayor of Mana Village, and along with Watts, a dwarf, ask him to investigate these 3 places. So he does, and finds 3 bosses at each one. After the task in Lorimar is finished, The strange man appears yet again and introduces himself as the Mana Lord. As all barriers are destroyed, the lord takes the sword and brews up a storm in the land of Wendel. He then disappears- the player then goes to Wendell, and sees the lord once again. The Lord is about to kill him- when a group of Gems appear around him to block attack.
Deciding he must kidnap Tess, he does so and vanishes. The player then heads to the ruins, where at the bottom he fights the shadows of his former family. After defeating them, he then sees a Toy Horse, which seems to be of no purpose. He/she takes it, however. Adventuring on, the player tries to find the Path of Life, under the roots of the Mana Tree. The place is sealed- however, the Toy Horse found in the other room opened up the door. The end of the path reveals the Mana Lord.
However, he is defeated by the player, and admits that he never meant to harm anyone. He then further admits that he was one of the children of mana from long ago. Giving back the Sword of Mana, he jumps off of a cliff, trying to reastore peace to the world. The shift in power causes a rift to open in the sky, where the second Child of Mana is. Destroying this monster, the player has then ultimately saved the world. Tess and the player are then entrusted with the care of Illusia, while everyone else there must leave. Humans wont return for many years-They make for Jadd, to start a new life.
- Ferrick - A fifteen year old boy who lost his family in the Great Disaster. His main weapon of choice is the Sword.
- Tamber - A sixteen year old girl dancer. She also lost her family in the Great Disaster. Her main weapon of choice is the Bow.
- Poppen - A nine year old boy. He lost his father in the Great Disaster and his mother at birth. His weapon of choice is the Flail.
- Wanderer - A traveling merchant whose age is unknown. He is part of the Niccolo Tribe. His weapon of choice is the Hammer.