Picking up the story during the events of the previous game, The Lost Age puts the player into the roles of a magic-attuned "adept" named Felix and his allies as they seek to restore the power of alchemy to the world of Weyard. Along the way, the player uses magic to defeat enemies and discover new locations, help out local populations, and find elemental djinn which augment the characters' powers.
Upon release, The Lost Age was generally praised, although many publications found that the game was not as good as Golden Sun. Nonetheless, IGN ranked the game as the eighth-best Game Boy Advance title of 2003 and the 22nd-best GBA game of all time. It has sold over 680,000 units.
Much of the time spent outside of battle takes place either in the game's overworld or within dungeons, caves, and other locales with puzzles integrated into their layout. Unlike the original game, in which the overworld was explored on foot except for a brief, non-navigable boat ride, a large portion of The Lost Age's gameplay involves navigating a magical ship across a large sea, visiting continents and islands. To complete puzzles, players must either push pillars to construct negotiable paths between elevated areas, climb up and rappel down cliffs, or obtain a special item to progress through the story and game world. Many of these puzzles revolve heavily around the usage of the game’s resident form of magic spells, Psynergy, requiring the player to find items that grant the bearer new forms of Psynergy in order to accomplish tasks.
Whereas many role-playing games limit the usage of their forms of magic to battles as offensive and defensive measures, Psynergy spells are also heavily used in puzzles and exploration. Some types of Psynergy can only be used in combat; conversely, some spells are only used in the game's overworld and in non-battle scenarios. Still other Psynergy can be used for both situations; for example, the “Frost” spell can be used to damage enemies in battle, or to transform puddles of water into elongated pillars of ice as part of a puzzle. Psynergy comes in four elements: Venus (rocks and plants), Mars (fire and heat), Jupiter (wind and electricity), and Mercury (water and ice). The player gains more and more Psynergy spells as the game progresses, either through levelling up or acquiring and equipping, or using, special items, and with each "utility" Psynergy spell the party gains access to more locations and secrets hidden within the game world. Players will be required to return to previous locations in the game to finish off puzzles which they could not solve earlier because of the lack of specific Psynergy spells. Players can transfer their characters and items from Golden Sun to The Lost Age by means of a password system or Game Link Cable, and players are rewarded for fully completing both games.
The Lost Age contains both random monster encounters and compulsory battles, which advance the story. When a battle begins, a separate screen is brought up where the enemy party is on the opposing side and the player’s party is on the battling side. While battle is conducted, the characters and background swirl around and change positions in a pseudo-3D effect.
Gameplay in relation to The Lost Age's battle mode is similar to traditional console RPGs. In each battle, the player is required to defeat all the enemies using direct attacks with weapons, offensive Psynergy spells, and other means of causing damage, all while keeping their own party alive through items and supportive Psynergy that restore life and supplement defense. If all the player's characters are downed by reducing their hit points to zero, it is considered “Game Over”, and the party is returned to the last village that the player visited and suffers a monetary penalty. The successful completion of a battle yields experience points, coins, and occasionally rare items.
In addition to the main game itself, there is also a competitive battling mode accessible from the menu screen, where players can enter their currently-developed team from their saved game files into an arena where they can battle increasingly difficult CPU-controlled enemies or other players head-to-head to see which of their team setups are stronger. In both cases there are no experience points or coins to be earned.
Collected Djinn are always assigned to a character of the player's choice, and can be either set, standby or recovering. When a Djinni is set, that Djinni exerts influence on its corresponding character’s class, statistics and Psynergy collection depending on both the character’s innate element and that of the Djinni. In combat, the player can choose to have a character use a set Djinni during that character's turn. Each Djinni has its own special effect when invoked during combat. These effects include enhanced elemental attacks, buffing or debuffing, healing, and other effects. After using a Djinni, its status is changed to standby. While standby, Djinn do not contribute to a character’s class, but can be used for Summon Sequences, where the player summons a powerful elemental monster. This is the game’s most powerful method of attack, and also the riskiest, as it requires Djinn to be on standby and therefore not available to bolster the statistics of whichever character the Djinn is equipped to. Once a Djinni on standby has been used for a Summon Sequence, it takes a number of turns recovering before it restores itself to set position on a character. There are a total of 29 Summon Sequences in The Lost Age; 16 from the previous game can be used alongside 13 new sequences, each of which must be earned individually, for instance some are acquired by defeating optional bosses.
There is a total of 72 Djinn encompassing the four elements, that can be mixed and matched to the eventual eight characters in almost any manner, making for a large array of possible class setups for all eight playable characters, allowing a variety of combat options.
Several groups of characters serve as Felix's antagonists in The Lost Age. He is at odds with the heroes of the original Golden Sun, led by the young Venus Adept warrior Isaac, who pursue him across Weyard under the belief that Alchemy would potentially destroy Weyard if unleashed. One of Saturos' original companions, a powerful and enigmatic Mercury Adept named Alex, allies himself with a second pair of powerful and imposing Mars Adept warriors, Karst & Agatio. They keep the pressure on Felix to ensure he proceeds with his quest as he is supposed to.
The antagonists of the previous game, Saturos and Menardi, have been slain in battle by the game's protagonists led by Isaac, but not before the pair succeeded in activating two of four great lighthouses situated across the world of Weyard, the Elemental Lighthouses. But now Saturos' remaining travelling companion, Felix, has taken the rest of Saturos' group and now sets out on a journey of his own to complete Saturos' original objective to activate the remaining two Lighthouses, for lighting all four will achieve the restoration of the powerful force of Alchemy to Weyard. Sailing the oceans of Weyard on a ship with their new companion Piers, Felix and his party embark on an epic expedition while pursued by Isaac's party.
Eventually, Felix's party is able to achieve entrance 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 has always been 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. Knowing that restoring Alchemy is what must be done to actually save the world, Felix sets out to climb and activate Jupiter Lighthouse. But when Isaac's pursuing party enters the lighthouse, they are trapped and ambushed by the vengeful Mars Adept Warriors, Karst and Agatio. Felix comes to assist Isaac to defeat Karst and Agatio.
Felix is finally able to explain to Isaac why Alchemy's release is a necessary thing for everyone, and that Saturos and Menardi were aiming for this goal merely for the sake of the survival of their home colony of Prox to the far north, located near the Mars Lighthouse. Felix and Isaac's two traveling parties join forces to form one unified group that sets out north to activate Mars Lighthouse; however, when they reach the tower's top, the Wise One, the entity responsible for originally tasking Isaac to prevent the breaking of Alchemy's seal, confronts them. He warns them that mankind could very well destroy Weyard themselves if they had possession of such a power, and when Isaac insists on breaking the seal regardless the Wise One summons a giant, three-headed dragon for the party to battle in the final struggle.
When the party of Adepts have slain the dragon, they discover that the Wise One had transformed Isaac and Felix's parents into the, now-dead, beast." After a short period of mourning, they gather the resolve to finish their objective and activate Mars Lighthouse; with all four towers across Weyard lit, the process that heralds the return of the force of Alchemy to Weyard ensues at the mountain sanctum Mt. Aleph. Alex is there, however; he took advantage of everyone else's quests so that he would gain immense magic power for himself when Alchemy is unleashed. Unfortunately for him, though, the mountain collapses and sinks into the ground with him still on it. The Adepts, in the meantime, find that their parents have actually been revived by Alchemy's return, just as the Wise One originally planned. They are able to recognize that the reason the Wise One appeared to play that cruel trick on them before was to test their resolve as Adepts, and therefore test their ability to handle a great new responsibility: To ensure that throughout the world the newly released force of Alchemy is not abused by Weyard's populace like it was in the ancient past.
The lack of updates on any new releases following The Lost Age propagated several hoaxes. This included the unveiling of a Nintendo DS game called Golden Sun: The Solar Soothsayer, which was reportedly shown off at a small pre-E3 2007 gathering. After this was decried as a hoax by official sources, the hoax's author confessed he made it in order to generate more discussion about the series and a sequel. The Takahashi brothers commented in October of 2007 that they still want to make a third Golden Sun title, going so far as to say that they "have to" and that Nintendo had asked them to make another. They claimed that they have not because they wish to give the title the development time it deserves. In April 2008, Nintendo Power magazine interviewed Shugo Takahashi on one of his latest games. When questioned regarding a third Golden Sun, Takahashi replied "A new Golden Sun? Well, I personally think that I want to play a new RPG, too...
IGN gave the sequel high marks, noting that even though the game is not a sequel in the traditional literary sense, it was still an excellent game. While most of the game mechanics remained unchanged, the addition of more complicated puzzles was welcomed. The Lost Age subsequently became IGN's "Game of the Month" in April 2003. Shane Bettenhausen of Electronic Gaming Monthly argued that though The Lost Age is "not going to win any originality contests (this looks, sounds, and feels nearly identical to its predecessor), but when more of the same means more top-notch roleplaying, I can't complain". Other publications singled out the graphics and audio as particularly strong features.
Some publications found fault with complaints which remained from the original, including the combat system. IGN and GamePro took issue with the lack of "smart" combat; if an enemy is killed before other party members attack it, those members switch to defense instead of intelligently attacking the remaining enemies. Ethan Einhorn of GameNOW felt that the only elements that set the fighting system above "typical RPG fare" were the graphics. GameSpy felt that Camelot could have added more features, and criticized the long opening sequence which either alienated players of the previous games, or confused new players by swamping them with unfamiliar places and characters.
The Lost Age sold 96,000 units in its first week in Japan, being the best-selling game of the period. The game sold a total of 249,000 copies in Japan and 437,000 in North America by November 21, 2004.