Golden Sun

While each of the three Golden Suns have different stories, the overall story follows a group of Psynergy-wielding-Adepts on the quest to save the world. These quests are intimately tied in with Alchemy. 
 

Golden Sun

Isaac is the main character of Golden Sun. In the prologue that occurred three years before the game, a boulder rolled down from the top of Mt. Aleph towards the small town of Vale. The town vastly survived the incident, but Isaac's father, as well as the parents and brother of his  friend Jenna, disappeared after the incident and were thought dead. Feeling as if he could have protected his father, Isaac takes up the study of Psynergy, in order to become stronger.  
 
Three years later, when his friends Jenna and the scholar Kraden were kidnapped, and the sacred treasures of the Sol Sanctum, the Elemental Stars, were stolen, he and his best friend Garet are thrust into a quest to stop the Elemental Lighthouses from being lit. The Wise One, eye-shaped, god-like protector of the Sol Sanctum, revealed to Isaac and Garet that the Stars would light the Lighthouses, and by lighting the Lighthouses, Alchemy would be restored to the world, dooming mankind. Entrusting the only Elemental Star that was not stolen, the Mars Star, to Isaac and Garet, the Wise One set their quest in motion.  
 
With this burden, Venus Adept Isaac and Mars Adept Garet set out to intercept the thieving Saturos, Menardi, Jenna's traitorous brother Felix (also a Venus Adept), and the mysterious Mercury Adept Alex. Along the way, Isaac and Garet are joined by the Jupiter Adept Ivan and the Mercury Adept Mia. However, they were unable to prevent the lighting of the Mercury Lighthouse or the Venus Lighthouse. However, Isaac's party managed to fell Saturos and Menardi at the conclusion of the first game. 
 

Golden Sun: The Lost Age

Felix is the main character of Golden Sun: The Lost Age. Starting at the end of Golden Sun, Felix, Jenna, the Jupiter Adept Sheba (also kidnapped by Sarturos' group), Alex, and Kraden were stranded on an island after the Venus Lighthouse was lit, and, due to the resulting earthquakes, drifted to the other side of the world. After gaining their bearings, recruiting the Mercury Adept Piers, and obtaining a ship, it is revealed that Alchemy is necessary to the world of Weyard.  When the ancients had sealed up Alchemy, they stopped people from abusing it, but as Alchemy held the world together, they cursed the world with a slow death. Because of that slow death, the town of Prox, Sarturos and Menardi's hometown, was drifting towards the edge of the flat world.  
 
Making haste, Felix's party made its way to the Jupiter Lighthouse. There, they saw Isaac's party under attack by Agatio and Karst. Also from the far-off town of Prox, Karst wanted to defeat Isaac, Garet, Ivan, and Mia, because they killed her sister, Menardi. Surprisingly, Felix came to Isaac's rescue, but the Jupiter Lighthouse was lit. Furthermore, Karst and Agatio had stolen the Mars Star from Isaac. 
 
Retreating to the nearby town of Contigo, Isaac and his friends confront Felix, and learn the truth about Alchemy. After absorbing what Felix, Jenna, Sheba, Piers, and Kraden claimed, Isaac accepted the necessity of Alchemy, and joined Felix and his party on their quest. As such, their next destination was the Mars Lighthouse, which was completely frozen over. While attempting to re-heat the tower, the party fought two Flame Dragons, which turned out to be a horribly mutated form of Agatio and Karst. In their dying breaths, they said that "the eye" deemed them lacking the will to proceed. Before they passed away, the two entrusted the Mars Star to Felix, asking him to complete the job. 
 
Making their way to the top of the Lighthouse, Felix, Isaac, and the rest of the Warriors are confronted by none other than the Wise One. The Wise One chastises Isaac and Garet for not heeding his orders and assisting in the return of Alchemy. When the group reveals what they have learned, the Wise One notes how they have been played for fools. In reality, Alex, the Mercury Adept who had assisted Saturos, Menardi, Karst, Agatio, and Felix, knew more than they did. Once the final Lighthouse was lit and Alchemy was restored to the world, the power would converge in a "Golden Sun" at the top of Mt. Aleph. Alex was approaching the top to absorb this power.  
 
Though shocked, the group of Adepts maintained their resolve, and cited something the Wise One had said: He was unable to interfere with them directly. The Wise One noted this, but causes a "miracle" to happen, and summons a Three-Headed Dragon. In their most fearsome battle, the Adepts defeated the beast. At the conclusion, however, they had really slain Isaac's father and Jenna and Felix's parents. After the incident at Mt. Aleph, they were not dead, but rather, found by Sarturos and Menardi and imprisoned in Prox. Sad, but maintaining their resolve, the group threw the last Star into the Lighthouse and restored Alchemy. 
 
However, the Wise One never intended for their parents to die - the rush of energy that emerged from the Mars Lighthouse revitalized their parents, and restored their lives. Happily, the group returns to Vale, only to find it completely destroyed by the Golden Sun. But no one had died. The Wise One informed the citizens of Vale about how the Golden Sun would destroy their homes, and they fled. With everyone alive, the Adepts, later called "The Warriors of Vale," lived with their loved ones. 
 

Golden Sun: Dark Dawn

Rather unfortunately, Alchemy stopped the world from a slow death, but caused numerous natural disasters. Taking place 30 years after The Lost Age, Matthew, the son of Isaac, is the main character of Golden Sun: Dark Dawn.