After a magical boulder devastates an isolated village beneath Mt. Aleph, a series of events unfolds that may lead to the dangerous practice of Alchemy falling into the wrong hands. A Psyenergy student named Isaac, and a group of his friends, head out to study - and ultimately reclaim - the misplaced magic.
Taking the form of a traditional RPG, Golden Sun splits into a top-down adventure, and group battles. The top-down adventure lets your characters solve puzzles, search for items, interact with characters, and so on. The battle mode sets you against an enemy or group of enemies and allows your characters to fight using the items and weapons they have acquired.
Outside of Colosso is a fountain filled with turtles and crabs. If you throw coins at them, they change color. This appears to be referencing the arcade Mario Bros., where turtles and crabs would change colour when hit.