This is a moderately detailed overview of the story progression through Golden Sun and Golden Sun: The Lost Age. Details are presented as they are revealed in each game. For the story as each element happens in chronological order, see Golden Sun timeline.
Golden Sun
Background
Ages ago, in the world of Weyard, the omnipotent force of Alchemy provided all manner of culture and power to its people. When harnessed, Alchemy could achieve fantastic effects of any scale, examples of which were the transmutation of lead into solid gold and the ability to thwart death itself. Civilizations and technology developed to great levels, but eventually, the ambitions and aspirations of some individuals developed the same way, leading up to power struggles and eventually a world war, where Alchemy was increasingly abused as a military weapon, and the prize for the victor was dominion over Weyard with control over Alchemy’s powers. Weyard was nearly demolished.
Eventually, a group of wise men known as the Sages convened and made a vital decision for Weyard’s welfare: They sealed Alchemy away for what would undoubtedly be many ages, within a vessel of stone, the Stone of Sages, hidden in the darkest depths of Mt. Aleph, site of a shrine to Sol and Luna. The world was deprived of a giant resource, but it was saved from the destructive tendencies of its inhabitants. The Sages, though, did not believe in permanent withdrawal of the force, so they decreed the construction of an intricate system of locks and keys situated throughout Weyard, and this system would comprise of four great towers as the locks (called Lighthouses) and four jewel-like crystals (called Stars) as the keys, and each respective pairing of Star and Lighthouse would represent one of the four elements of the world: Venus, Mars, Jupiter, and Mercury. With the elemental stars hidden away within Sol Sanctum, Weyard remained inactive and Alchemy remained dormant underneath Mt.Aleph for ages.
As the ages passed, a town called Vale would develop at the foot of Mt. Aleph. The inhabitants soon made it a point to be the guardians of Sol Sanctum and Mt. Aleph. Due to the town’s proximity with Sol Sanctum's secret, the inhabitants developed an adeptness to Psynergy, the art of channeling the energies of the four elements into a form of magic. Psynergy came in the forms of the four elements, as Venus (control of the earth's plantlife and rock formations), Mars (manipulation of heat and fire), Jupiter (projection of wind and electricity), and Mercury (power over water and ice). The Adepts, as users of Psynergy were called, knew never to reveal their craft to any outsiders who might pass through the village, and also to refrain from entering Sol Sanctum freely, so as to preserve the sanctity of the shrine. This was their duty for a long period of time, until the present, where the story of the game begins.
The Process of Alchemy
Three years before the present, a pair of menacing, scale-skinned Mars Adepts named Saturos and Menardi arrive from a Mars Adept colony in the far north, attempting a raiding expedition upon Mt. Aleph. Their aim was apparently to steal the Elemental Stars inside for a plot of theirs. However, they failed to solve the riddle blocking their way and triggered a trap, causing a defense mechanism to project a terrible thunderstorm around Mt. Aleph that in turn caused a giant boulder to be dislodged and crash through the town below, seemingly killing several of its inhabitants. The pair knew that though they failed for now, they would attempt Sol Sanctum again in the future.
Three years to the present day, Isaac, a young Venus Adept, has lived in relative tranquility in Vale with his friends Garet and Jenna, both young Mars Adepts, and Kraden, an elderly scholar researching the ancient art of Alchemy though not an Adept himself. Isaac’s father and all of Jenna’s immediate family -— her parents and her brother Felix —- had died in the boulder tragedy three years prior. Isaac and his friends agree one day to assist in Kraden’s ambitious research venture to explore Sol Sanctum and study the Stars inside, despite the fact that it is off limits by the town legislature. But the four enter the Sanctum and explore its sacred corridors, eventually finding the chamber where the four Stars await on pedestals. Kraden has Isaac and Garet fetch the four stars for him to study.
Fate suddenly plays a major twist in the lives of all involved. Saturos and Menardi appear and apprehend Jenna and Kraden, demanding that Isaac hand over the Elemental Stars. Saturos is accompanied by two other accomplices: Alex, a debonair Mercury Adept with apparently strong Psynergy talents, and none other than Felix, Jenna’s long-lost brother, who Saturos explains was saved by him after the boulder disaster three years ago, and is now part of their quest to activate the Lighthouses and restore Alchemy to the world. Isaac and Garet are understandably as shocked as Kraden and especially Jenna, but they have no choice but to comply with this group’s orders and give them the Elemental Stars.
Suddenly, due to the removal of the Elemental Stars from their pedestals, the entire area starts trembling under the influence of a volcanic eruption, and Saturos’ group is forced to flee with only three of the Stars, leaving Isaac and Garet to potentially die. In the case that they might survive, Saturos takes Jenna and Kraden as hostages for Isaac to follow, so that they could get the fourth star. However, Isaac and Garet soon come face-to-eye with the monolithic guardian of Mt.Aleph, the Wise One, who declares that the effort to restore Alchemy constitutes a threat to the world, so thus he tasks Isaac and Garet to prevent Saturos from activating the Elemental Lightouses, and he returns the two boys to Vale as Mt. Aleph erupts, saving them.
Later, Isaac and Garet explain everything that transpired in Sol Sanctum at a town meeting in Vale, relating the command of the Wise One to chase Saturos’ band and prevent him from unleashing the apparently deadly consequences of Alchemy’s return. After measuring all circumstances involved, including the capture of Kraden and Jenna by apparently her own brother Felix, the townspeople agree that the responsibility falls on Isaac and Garet to set out on this urgent quest and save all of Weyard. Thus do Isaac and Garet depart from their hometown and embark on the adventure of a lifetime.
The Mercury Lighthouse
Early in their hasty journey, Isaac and Garet meet and accept the Jupiter Adept boy Ivan as part of their party, and the three of them head off into the direction of the nearest Lighthouse, the Mercury Lighthouse, because that would easily be Saturos’ first target. Upon reaching the village of Imil, located in front of Mercury Lighthouse, Isaac meets Mia, a young female healer who is revealed to be a Mercury Adept and one in charge of guarding the Mercury Lighthouse. Mia joins Isaac and his party as they enter the towering structure and climb to its top, the Mercury Lighthouse Aerie, intent on preventing Saturos from activating it. They find, however, that they are too late: Saturos has already activated Mercury Lighthouse, having cast the Mercury Star down the tower’s throat. Isaac, Garet, Ivan, and Mia all engage in battle with Saturos, who proves to be a menacingly powerful adversary. However, because they are battling in the vicinity of the newly activated water-elemental Lighthouse beacon, Saturos’ fire-based powers are suppressed enough for Isaac to defeat him.
However, Alex appears and reveals to Mia that he is in league with Saturos, and Mia is instantly horrified because Alex once shared her objective to prevent the Mercury Lighthouse's activation as a fellow Mercury tribesman, but he now seems to have undergone a revelation, having betrayed his charge of duty. Alex seems to have decided that returning the powerful force of Alchemy, a force he obviously admires, to Weyard is more desirable than keeping the force locked up. After Alex helps Saturos up and they both depart, Mia, drained by Alex’s betrayal, decides to join Isaac’s quest to prevent Saturos and Alex from lighting the remaining three Lighthouses, and Isaac’s complete party now departs from Imil in his continuing quest to stop Saturos.
The Venus Lighthouse
For the next great period of time, Isaac’s party travels around the entire mainland continent of Angara, helping the troubled villages they encounter along the way. Soon they take a ferry service to the neighboring southern continent of Gondowan, a voyage that proves none too pleasant due to sea monsters such as the Kraken on the attack. They then arrive in the bustling metropolis of Tolbi, under rulership of the mysterious Lord Babi. After competing in and winning this year’s annual tournament of warriors, Colosso, Isaac proves himself capable of embarking on an additional quest to help Babi that involves locating the mythical island city of Lemuria somewhere in the ocean and retrieving some special draught for him. Babi grants Isaac eligibility to use his personal sailing ship for this quest in the near future. The ship in question is hidden within the town of Lalivero, near the Venus Lighthouse, which is Isaac’s next destination at any rate.
However, after traveling east through a desert to reach Lalivero, Isaac finds that Saturos’ band has captured a young Laliveran girl, Sheba, hostage as well, for reasons Isaac does not yet know. But Isaac plans to thwart whatever Saturos is scheming, so he enters Venus Lighthouse and climbs it in haste, soon reaching the Venus Lighthouse Aerie where, to his relief, it has not been lit yet. Isaac finds Saturos and Menardi criticizing Felix for his objections to their kidnapping Sheba, who is up there with him, and it is revealed to Isaac that Sheba is actually a Jupiter Adept just like Ivan. Isaac comes over to confront Saturos, and the cunning Mars Adept sees an opportunity and orders Ivan to hand over his Shaman’s Rod. Saturos explains that both Sheba as a Jupiter Adept and the Shaman’s Rod are required for him to climb and light Jupiter Lighthouse in the future. Ivan reluctantly gives Felix the Shaman’s Rod to ensure Sheba’s safety.
Saturos then decides that it is time for Isaac’s meddling party to die and he and Menardi launch a fierce offensive against them, but the combined swordplay and Psynergy teamwork among Isaac and his friends, which they developed over the course of their journey, eventually proves enough to defeat the two Mars Adepts. But in an underhanded tactic, Saturos drops the Venus star into the Venus Lighthouse’s gullet, instantly failing Isaac’s quest a second time. As the Venus beacon is activated, Saturos and Menardi are restored, and as a last stand against Isaac they execute their ultimate power: The merging of their bodies into a tremendous, two-headed Fusion Dragon. Isaac wages his fiercest battle yet, and soon he manages to slay the Fusion Dragon in an amazing victory over superior opponents. Defeated, Saturos and Menardi seemingly die as they fall into the abyss of the gullet.
Felix and Sheba watch stunned on the sidelines, and suddenly the energy of the newly lit Venus beacon causes an earthquake, causing Sheba to fall off the lighthouse and into the sea below, and Felix jumps after her in what can be described as affection-driven furor. To Isaac and his party, their victory at Venus Lighthouse is empty because they failed to prevent the firing up of the second Lighthouse Beacon, so they return to the ground level.
Back in Lalivero, Isaac convenes with Sheba’s adoptive family, and they conclude that Felix and Sheba are still alive and are with Alex, Jenna, and Kraden, all continuing to be part of the effort to light the remaining two Lighthouses, Jupiter and Mars. Isaac, of course, can’t understand why his old friend Felix would have such a strong desire to release, according to the Wise One, a force that could devastate all of Weyard, but as far as Isaac can tell Saturos and Menardi were under the belief that Alchemy would reinvigorate and change the world, somehow. But Isaac and his party know from their encounter with the Wise One that they must prevent it from happening, lest the world be subjected to destruction.
Isaac soon finds the sailing ship that Babi hid in Lalivero, the ship that Babi wanted Isaac to find and commandeer for himself on his subquest for Babi. With this ship, Isaac can continue his quest on a new front, exploring the oceans of Weyard and searching for Felix and Alex’s band, so as to thwart their plan for unleashing Alchemy, set them straight, and save Weyard.
Golden Sun: The Lost Age
The Great Eastern Sea
Golden Sun: The Lost Age begins moments before the finale to the previous game in the series at Venus Lighthouse, but from Felix and Jenna’s shared perspective. When their holders Saturos and Menardi are slain at the aerie of the newly activated Lighthouse by Isaac and his party of Garet, Ivan, and Mia, a series of cataclysmic, chaotic events drive Felix, Jenna, and their partners Sheba, Kraden, and Alex away from the tower upon a floating peninsula that eventually crashes into the foreign continent to the south. Alex leaves for himself while the remaining allies gather and postulate their next courses of action; Since the remaining two Elemental Lighthouses on their journey to restore the omnipotent force of Alchemy to the world lie in the Great Western Sea and in the far north of Weyard, they will need to find a ship somehow in order to sail to these locations. Felix, Jenna, Sheba, and Kraden form a new traveling party and set out on a great journey of their own, the search for a ship being the first order of business.
Early in their search for a ship, Felix’s party comes across Piers, a man who is revealed to be not only a Mercury Adept, but a former resident of the legendary hidden society of Lemuria, located within a secluded area in the middle of the Great Eastern Sea. Piers was driven out of his home by a tidal wave caused by the spontaneous appearance of the mythical entity known as Poseidon near Lemuria, and it is his objective to sail back into his home. Felix agrees to join Piers in his quest in hopes of getting a ship from Lemuria for his own objective afterwards. The journey that ensues becomes an extremely lengthy expedition across the entire eastern half of the world of Weyard, as Felix’s party traverses many exotic and arcane locales in search of pieces of the legendary Trident of Ankhol, the only weapon that can effectively combat Poseidon.
During their exploration, however, Alex reappears, and he is accompanied by some new characters hailing from the Fire Clan of the north: Karst, the vengeful younger sister of Menardi who Isaac slew at Venus Lighthouse, and her imposing partner-in-arms, Agatio. Karst takes this opportunity to make it clear to Felix that she plans on exacting her deadly revenge on Isaac for his sin, and that she will not tolerate Felix coming to Isaac’s aid once that time comes, regardless of how close Felix and Isaac were as kids earlier in their lives. Alex also takes this opportunity to “persuade” Felix’s group to keep the task of lighting the Jupiter Lighthouse as their priority because, since Felix is the one with the Jupiter Star, Alex does not appreciate Felix undertaking any time-consuming distractions that would cause him to stray from their mutual goal to return Alchemy to the world of Weyard. After Alex leaves with the two Mars Adepts, Felix knows in the meantime that he should still enter Lemuria before crossing into the Great Western Sea.
After successfully battling and defeating Poseidon in front of Lemuria with the Trident, Felix and his party proceed to enter the ancient society of Lemuria. They are brought to the chamber of the great king of Lemuria, Hydros, who welcomes Piers back warmly. Felix and Kraden explain their objective to restore Alchemy to Weyard, and Hydros in response displays evidence to support his long-standing suspicion of a shocking revelation: The landmasses of the world have been waning and shrinking into the oceans and the life force of the world has been diminishing over the ages, all on account of the absence of Alchemy. Therefore, Felix’s journey to activate the Lighthouse beacons that will break Alchemy’s seal proves more important than Felix had ever imagined. With this revealed, Hydros tasks Piers to accompany Felix and his friends on the rest of their journey to restore Alchemy and save the world from eventual collapse. Thus does the party depart in the direction of the Jupiter Lighthouse in the Great Western Sea.
The Jupiter Lighthouse
After trading the Shaman's Rod he took from Ivan for the Hover Psynergy spell necessary to climb Jupiter Lighthouse, Felix proceeds to climb the structure, intent on lighting it. While doing this, however, Felix witnesses a shocking sight: Isaac and his friends have also been climbing the tower in pursuit of Felix, but they were ambushed by Karst and Agatio, which separated Mia and Garet from the fray and forced Isaac and Ivan to engage Karst and Agatio alone. They ultimately lose the duel and are knocked unconscious. Before the Mars Adepts can finish them off however, Felix steps in and defiantly forces Karst to agree to spare Isaac’s life. In exchange, he takes the Mars Star from Isaac and then activates the Jupiter Lighthouse with the Jupiter Star. Karst begrudgingly accepts this offer. Isaac, seeing that Felix knows what he is doing, hands over the Mars Star willingly, and Felix proceeds to activate the Jupiter beacon at the top of the tower. While the rest of his party assists Isaac's group, Felix and Piers head for the top. But Karst and Agatio, feeling betrayed by Felix’s intervention, decide that he is no longer an ally and proceed to pilfer the Mars Star from him. However, Sheba and Jenna arrive in time to save him and engage the vengeful Mars Adepts in a fierce confrontational battle in front of the Lighthouse's beacon. Alex appears and prevents the two parties from slaying each other, reasoning that since the Mars Star is in Karst's possession, she and Agatio need to live in order to light the final Lighthouse to the far north, the Mars Lighthouse. Alex then leaves with Karst and Agatio.
Felix and Isaac, along with their respective parties, confront each other in a deserted house in the nearby town of Contigo. Isaac demands to know why Felix has been trying to return Alchemy to the world because Isaac is under the impression that it is a force that was originally sealed because it would destroy the world if released. Felix explains the truth about Alchemy as it was revealed to him in Lemuria, shocking Isaac with this reveal of the misguided nature of his own quest. Then Felix explains the real nature of the boulder tragedy that was set upon their hometown of Vale three years ago. It turns out that none of the supposed casualties of the disaster – Isaac’s father and Felix and Jenna’s parents – actually died, and they were in fact rescued (along with Felix) by Saturos and Menardi, after that duo’s failed initial attempt at Sol Sanctum. Their parents are in fact alive and well in the colony of the Mars Clan in the far north, but they were forced to remain there by Saturos and Menardi while they took Felix and Alex along for their quest to activate the four Lighthouses, and the two late Mars Adepts had promised to set them free once all four were lit. That was the reason why Felix joined Saturos: to save his parents.
Having come to an understanding about their common goal, Felix and Isaac join forces to form a traveling party of nine (including Kraden). However, the oracle of Contigo reveals that Karst and Agatio will fail in their attempt to activate the Mars Lighthouses, and not only that, the activation of the Lighthouses of Mercury, Venus, and Jupiter has caused an imbalance against the element of Mars (fire), causing Weyard to experience a global chill that is increasing by the hour. This adds a sense of urgency to Isaac and Felix’s quest, for Weyard may freeze if the natural balance is not restored in time, so they set out northward to Mars Lighthouse to reunite with their parents and save both the world’s lifeforce and climate.
The Mars Lighthouse
Crossing into the northernmost reaches of Weyard, Isaac and Felix’s party makes it to the settlement of Prox, the hometown of Agatio, Saturos, Menardi, and Karst. The residents of Prox are of the same scale-skinned race as these four, but they certainly are not evil; indeed, they are clinging onto life themselves, under the influence of extremely harsh, frigid weather. Isaac communicates with the natives and learns of the motives behind Saturos’s original attempt on Sol Sanctum so long ago: The Proxeans had long since known that Alchemy was the source of Weyard’s life, because currently the edge of the world just up north is creeping closer to the town, an expanding abyss that owes its existence to Alchemy’s absence. Therefore, the town’s legislature had decided years ago to try and save both their town and the rest of the world by sending its two finest soldiers, Saturos and Menardi, out on a global quest to restore Alchemy. Isaac now understands that the two Mars Adepts who he slew at Venus Lighthouse, as obsessed as they were, were trying to be heroes themselves, thinking only of their endangered hometown. But now Isaac knows that it is up to him, Felix, and the rest of their friends to activate the Mars beacon and save the world from eventual collapse. Thus do they head to Mars Lighthouse and begin the final portion of their quest.
During their exploration of Mars Lighthouse, the group encounters two large Flame Dragons, which they quickly dispatch. However, the dragons transform and reveal themselves as the ruined bodies of Karst and Agatio, both near death. Karst explains that some mysterious force came in their way and turned them into dragons, preventing them from activating the Mars Lighthouse with the Mars Star, which Karst gives to Felix before dying. With the Mars Star back in their possession, Felix and Isaac head upward to the very top of the Mars Lighthouse.(If you return to the room in which you fought the dragons and actually slain Karst and Agatio, you will notice thier bodies have dissapeared.)
At the aerie of Mars Lighthouse, the Adepts come face-to-eye with none other than the Wise One, the entity responsible for pitting Isaac and Garet against Saturos and Felix’s effort to restore Alchemy to the world from the start. The Wise One is irate at Isaac for disobeying his command, but Isaac declares that he knows the truth about Alchemy and how it is necessary for the world to survive. The Wise One counters with the foreboding fact that Alchemy, if returned, would inevitably be abused by the populace of Weyard, and he supports his claim with a revelation that horrifies all: Alex has duped them all, having carefully guided and influenced everyone involved in the effort to restore Alchemy so that when the four Elemental Lighthouses are lit, they would merge their core essences into a single sphere known as the Golden Sun, which in turn would enter Mt. Aleph below to initiate the return of Alchemy—and Alex would be there to absorb the Golden Sun’s essence for himself and gain godlike powers. While everyone, especially Alex’s clanmate Mia, is mortified by Alex’s truly underhanded tactic for self-gain, Isaac knows that whether their quest accomplishes Alex’s aim is negligible; Restoring Weyard’s sustenance and stability outweighs all else regardless.
But the Wise One would rather make the Adepts fight for the right to light Mars: He summons the gigantic, three-headed Doom Dragon for them to battle before disappearing. The fiercest battle for the Adepts ensues in earnest, and the Doom Dragon is ultimately slain after a lengthy, harrowing conflict. Like what happened with Karst and Agatio, however, the dragon transforms into the ruined bodies of three people, and their identities constitute a grievous revelation of the worst degree: The Adepts have destroyed none other than their own parents, the ones they hoped to reunite with in Prox after completing their quest. They curse the Wise One’s name for his cruel act of deceit. Kraden, knowing that the end of their journey is at hand, convinces the Adepts that the sacrifice of their parents should be taken as the price that was necessary to save the lives of millions throughout the world, and Felix agrees and therefore casts the Mars Star into the Mars Lighthouse well.
Return of Alchemy
The Mercury, Venus, Jupiter, and Mars lighthouses are lit, and their beacons merge their lights into one focal point in the airspace of Mt. Aleph, forming the Golden Sun. In turn, the Golden Sun shoots out a ray that pierces the mountain and activates the Stone of Sages within. With this, the world of Weyard and all its inhabitants are infused with the omnipotent force of Alchemy, and as a result the climate is re-stabilized and the world’s inner life force is renewed.
Alex stands at the peak of Mt. Aleph, standing in the center of the Golden Sun’s stream of Alchemy-based energy into the mountain as it passes through his body. Once it ends, Alex is ecstatic with his newfound power and near-limitless life, and he is all too eager to test his power. He therefore attempts to summon a thunderstorm to attack Vale at the mountain’s foothills below, but the storm fails to manifest. The Wise One appears and explains to Alex that he has not gained the entirety of the Golden Sun’s power, for the Wise One took precautions to counteract Alex’s would-be attempt at dominion. Alex may possess the majority of the Golden Sun’s power, but the rest has entered Isaac’s body, leaving Alex’s mastery of Alchemy incomplete. Gravely disheartened and enraged that Isaac and the Wise One have robbed him of his dream, Alex attacks the Wise One with the power he has, but the guardian seems to paralyze him to the ground. Then the mountain and the surrounding landscape suddenly mutate and collapse, and the Wise One abandons Alex, saying that he may not survive this reformation. Alex, unable to flee, seems to disappear into oblivion as Mt. Aleph sinks into the ground.
Meanwhile, Isaac, Felix, and their friends evacuate the Mars Lighthouse which is now exhuming excess Mars Psynergy, and the energy causes the miraculous revival of their parents. Isaac and Felix immediately bring them back to Prox, where they are nursed to health by the Proxeans. Now that Alchemy has returned and Prox has been saved from doom along with the rest of the world, the Adepts and their parents receive heartfelt gratitude from the Proxeans even as the townsfolk feel remorse for the fates of their fallen heroes Saturos, Menardi, Karst, and Agatio. After saying goodbye, the Adepts sail back to their hometown of Vale. However, upon reaching it, they behold one last tragedy: The town of Vale has been erased alongside Mt. Aleph, and all of its inhabitants, including Garet’s family, are believed to be lost. But suddenly, all of the townspeople of Vale, including Isaac’s mother, show up in perfectly sound shape, and they explain that the Wise One evacuated them out of Vale before the town was destroyed. A great bout of rejoicing ensues; everything turned out for the best.
Kraden is able to figure out that The Wise One, as an upper-tier being whose divine charge was to safeguard Alchemy’s seal, constructed a giant test of some sort through all this. The Wise One knew that Alchemy would be a destructive force if it was abused by humans like it was abused in the ancient past, so he subjected Isaac and all of his friends to the trauma at Mars Lighthouse to test their virtues to see if they carried the strength necessary of the role of guiding Weyard down the path of civilization and peace as opposed to the path of warfare and power struggles, and to that end Isaac and his companions have succeeded. They happily celebrate and the scene ends with Isaac and Kyle's reunion with Dora (Isaac's mother).