Golden Sun: The Broken Seal and Golden Sun: The Lost Age, from henceforth shortened to GS1 and GS2 respectively, were originally one game. Due to the GBA's limitations, Camelot had to decide either to split the game into two or sacrifice graphics and extra areas. Anyway, the series is predominantly about Alchemy and the Psynergy (magic) that Adepts use, their effect on the world and whether or not the world needs Alchemy at all.
GS1 has a prologue that takes place three years before the main game begins and it focuses on a terrible cataclysm that befalls the peaceful mountainside town of Vale. We're introduced to Isaac, Garet, Jenna and Felix as they and their parents deal with the catastrophe. Isaac's father, Jenna's parents and Felix all perish that day. A mysterious man and woman are overheard conversing about how they started the event and, after Isaac and Garet get owned, we skip forward to "present day".
Isaac, Garet and Jenna meet up with Kraden, a scholar, to investigate and explore Mt. Aleph. During the course of their expedition, they eventually meet the mysterious man and woman inside a hidden room within the mountain. This room holds the Elemental Stars, four gemstones of unimaginable power that hold the key to lighting the Four Lighthouses. With Saturos and Menardi is, much to everyone's surprise, Felix. Another man, known as Alex, is also with them. Isaac and Garet gather and present the Elemental Stars to Saturos and Menardi, but are unable to give them the Mars Star because Mt. Aleph is about to erupt. To ensure Isaac and Garet will bring them the stone, Saturos and Menardi kidnap Jenna and Kraden. Isaac and Garet are then tasked by the Wise One (giant floating rock with a big eye in the middle) to not only save their friends, but to stop Saturos and Menardi from lighting the Lighthouses.
Over time, Isaac and Garet gain two more comrades - Ivan and Mia - as they eventually find themselves at the first Lighthouse. Even though it is a four on one battle and Saturos is greatly weakened by the Mercury Lighthouse, Isaac, Garet, Ivan and Mia fail to prevent him from lighting the Mercury Lighthouse. So off they go, chasing after Saturos and Menardi. After weeks of travelling across deserts and mountains and really big lakes, Isaac and his allies eventually find their way to the Venus Lighthouse in time to try to prevent Saturos and Menardi from lighting it. Proving how much stronger they have become, Saturos and Menardi combined are no match for our heroes. Even after transforming into a giant two-headed dragon, Saturos and Menardi fall. Sadly, Isaac and his friends could not prevent the Venus Lighthouse from being lit.
GS2 starts here, with a dramatic change in perspective. The game begins in Jenna's perspective within the Venus Lighthouse, mere moments before Isaac and his friends kill Saturos and Menardi. Jenna and Kraden find their way to the Idejima Peninsula, meet Alex, and wait for Saturos and Menardi there. They can only watch as the Venus Lighthouse is lit and the peninsula tears itself from the continent and drifts to the sea. Felix and Sheba (Sheba originally being a minor character that is kidnapped by Saturos and Menardi for being a Jupiter Adept like Ivan) somehow find their way onto the island, Felix having apparently swam to it, and eventually the island slams itself into a new continent. Perhaps the most unique change so far, however, is that Felix, Jenna, Sheba and Kraden want to light the remaining two Lighthouses. If they don't the world will die, effectively making Saturos and Menardi good guys.
The first order of business is to get a boat which, after a lot of messing about (interrupting a tribal ceremony, beating up pirates, hanging out with werewolves, traversing deserts and gaining a new ally in the form of Piers), is accomplished. As they do so, they meet two new characters called Agatio and Karst, who perform the same role as Saturos and Menardi once did but remain largely passive. Anyway, the party must travel to a hidden civilisation called Lemuria, Piers is from there, and only by visiting his home can the party proceed with their original plan. They find out while there that the world was once incredibly abundant in Psynergy but that four "wise" Sages created the Elemental Lighthouses and locked Alchemy away to prevent its misuse. Sadly this has caused the world to slowly corrode and die as you could call Alchemy the world's "blood". Their resolve now renewed, the party travel to the far West to light the Jupiter Lighthouse.
When they arrive, Isaac and his friends are there to stop them. Felix and Jenna want to try to explain everything to their friends. Agatio and Karst, however, have other plans. Knowing they could not defeat all four, Agatio and Karst split Isaac and Ivan from Garet and Mia and take them on separately. To protect them, Felix takes the Mars Star from Isaac and heads to the top of the Jupiter Lighthouse in order to light it. While there, he is attacked by Agatio and Karst who believe he has betrayed them. As his battle continues, Jenna, Piers and Sheba all show up and fight by Felix's side. With the Jupiter Lighthouse now lit, Agatio and Karst leave Felix and the others in order to complete the mission.
After some explaining, Isaac, Garet, Ivan and Mia join Felix, Jenna, Piers and Sheba. They're told that Agatio and Karst will fail to light the Mars Lighthouse and so the eight Adepts then travel north to the frozen wastelands of Prox to help them. As they climb the Lighthouse, the eight Adepts are set upon by two powerful Dragons. After defeating them, the two Dragons revert into their human forms and are none other than Agatio and Karst themselves. They truly did fail to light the Lighthouse and were transformed against their will. Taking the Mars Star, Isaac, Felix and the gang head to the top of the Lighthouse and find themselves confronting none but the Wise One himself. Enraged that Isaac would disobey him, but impressed by everyone's resolve, the Wise One gives the Adepts one final task. They must defeat a really big, three headed dragon. Garet laughs that three heads aren't much better than two, and the eight Adepts fight together for the last time.
Having defeated the giant Doom Dragon, and having realised that it was created from the thought-deceased parents of our protagonists, the Wise One reveals all. Alex, the man who had spurred on and guided the lighting of the Four Lighthouses the entire time, had engineered everything so that he could be at Mt. Aleph when Alchemy is finally reawakened and absorb the Golden Sun itself. The Wise One then leaves the Adepts and goes to confront Alex personally. After a brief battle, Alex is sealed within Mt. Aleph by the Wise One. Alchemy now free in the world and Alex now trapped under a mountain, GS2 ends on a happy note all ready for Dark Dawn.