Three years before the start of the game's main story, Saturos and Menardi raid Mt. Aleph with the intent to steal the Elemental Stars, but failed to solve the riddles guarding them and are driven away by the mountain's trap, a magically generated thunderstorm and rock slide. A few years later, Isaac, Garet, and Jenna join Kraden on his research trip to Mt. Aleph and manage to solve the shrine's puzzles and retrieve the Elemental Stars.
They are later attacked by Saturos and Menardi, along with Felix, a previous resident of Vale who was kidnapped during the storms three years earlier. They kidnap Jenna and Kraden and take three of the four Elemental Stars and depart to light the four lighthouses and release Alchemy on the world. Isaac's party is joined by two other young adepts named Ivan and Mia, and together they pursue Saturos' party in a lengthy chase and journey that follows eventually spans two continents, climaxing in a fierce battle that leads to Saturos and Menardi's death. With Saturos and Menardi killed, Felix convinces Jenna and Kraden to join him on an adventure to complete Saturos' original objective to activate the two remaining lighthouses that he failed to light. Joined by new companions Sheba and Piers, Felix and his party embark on an epic expedition while pursued by Isaac's party. Eventually, Felix's party succeded to enter into a legendary, secluded Atlantis-like society named Lemuria far out in the ocean. When they convene with Lemuria's ancient king, Hydros, they learn about Alchemy's true nature: it is the sustenance of Weyard's very life force, and its absence over the past ages has caused the world's continents to decrease in size and parts of the world to collapse into the abyss. Armed with this new information, Felix manages to persuade Isaac and his party to join them, and together they complete the goal of releasing Alchemy and preventing Weyard's eventual decay.
References in other games
Super Smash Bros. series
Elements from the Golden Sun games have made appearances in other media. Isaac, the main protagonist of the original Golden Sun game, is an unlockable "Assist Trophy" character in the Nintendo fighting game Super Smash Bros. Brawl. When he's summoned during battle by an Assist Trophy item, Isaac uses Psynergy to conjure a large hand three times in succession to knock the player's opponents off the stage. Should enemies attempt to evade, Isaac will turn in sync to attack a selected opponent. In addition, a medley of music from The Lost Age was selected to be on Brawl's soundtrack.
The game's sequel, Super Smash Bros. for Nintendo 3DS and Wii U, does not feature Isaac (Assist Trophy), but The Lost Age medley is featured along with the world map theme from Dark Dawn.