As one of several games in the series to make an appearance in the United States, Heroes of Mana takes place after the events in Seiken Densetsu 3, the Japanese sequel to Secret of Mana. Gamers take the role of Roget, a young pilot who is shot down while doing reconnaissance work over the enemy kingdom of Ferolia. Roget must make his way back to safe territory before enemy soldiers find him. During his journey he meets several allies that join his party. Players may adjust the skills and magical powers of characters including D'kelli, Qucas, and Yurchael to fit the needs of each mission.
Getting through the game takes more than RPG adventuring, and gamers must also gather Gaia stones to build unit-producing structures on Roget's ship. After manufacturing an army of troops, players can lead them into a mission along with 2-5 party members of their choosing. Navigating troops and individual players is done with slices of the stylus against the touch screen, and win conditions vary according to each quest. Players may find themselves destroying an entire army, taking down a specific target, or maneuvering to a point on the map. By connecting to a local wireless network gamers may create a custom match against a friend.