The story in Final Fantasy Legend II revolves around MAGI, the 77 shards of a shattered statue of the goddess, Isis. As a child, the main protagonist character is awakened by his or her father in the middle of the night, who explains he has to leave for a while. After leaving the protagonist with a MAGI and instructing the protagonist to never lose it, he makes his way through the protagonist's open window. Years later, having grown up, the protagonist decides to set out to find his or her father, learning he was part of a secret group called the Guardians hunting for the MAGI, fragments of an ancient statue that give power to their bearers. Accompanied by three friends, the protagonist sets out.

Exploring their world, they learn that there exist other worlds connected in a Celestial World by a winding twisting tower called the Pillar of Sky, and using MAGI they can use it to reach each world. They learn that new gods have risen to power in various places using the MAGI, and not all are benevolent to their surroundings. Seeking to become more powerful, the gods are looking for the other fragments, but the heroes learn that if all the fragments of the MAGI are brought together and the statue of Isis is reassembled, a terrible calamity will destroy all worlds.

Unlike the previous title of Final Fantasy Legend where defeat in battle means game over, in this game the heroes are brought before the god Odin where he offers to revive them if they are valorous and return to the same battle they were defeated in to try again. They may retry a battle as many times as they wish, but if the heroes refuse, then the game is over, only to restart at the last save; once the heroes defeat Odin himself in battle, they no longer have this option.

The heroes battle to collect the MAGI themselves while at the same time trying to retrace the lead character's father's path. They must battle with various foes and oppressive gods, including Odin who appears when the heroes are defeated and is encountered as an opponent later in the game. The heroes eventually reunite with the main protagonist's father at the Guardians' base, but the base is found and raided by the minions of aforementioned new gods and the father sacrifices himself to rescue an ally from a previous world being held hostage.

As the heroes have nearly collected all 77 MAGI, another character appears from one of the previous worlds to blackmail the group into turning over all their MAGI. Unable to pursue the villain due to being cut off from the Celestial World with no MAGI and fearing the destruction of the world is at hand, the protagonist's father reappears and reveals the Guardians spread misinformation about the MAGI and that there are actually 78. They join forces, recover the last MAGI, and re-enter the Celestial World to challenge the villain, who tries to release the full power of the Isis statue. Believing the combined power of the MAGI makes its owner invincible, the villain engages the heroes, but missing the last piece, the process goes awry and the villain succumbs to the power and explodes.

The father is mortally wounded in shielding the other heroes from the backlash of power, and the Celestial World and all the worlds connected to it tremble violently. The heroes decide to assemble the complete MAGI, hoping that its power can save the protagonist's father. The goddess Isis revives, notices the earthquakes, and after treating the hero's father (who remains unconscious), joins the party in descending to the center of the worlds where everything is now off balance. Upon reaching the center, a pair of massive mechanical Arsenals acting as a security system must be defeated to gain access to the core and stop the worlds from shaking.

The heroes learn that Isis was set aside by an ancient civilization to safeguard this pillar system, as the worlds would eventually become old and need to be repaired. Isis stays at the core, fixing the damage from the tremors, and the heroes return home with the protagonist's father. After the credits roll, the protagonist is awoken in the middle of the night by his or her father again much as in the beginning of the game, with the father saying he must leave again, this time on account of the Lost Ark (The Three Treasures in the Japanese version of the game). The main protagonist demands to come with him this time, and the father agrees. They begin to leave before they are stopped by the protagonist's mother who wants to join them and not be left alone again. They agree, the three of them leave through the open window, and the game ends.

Muses

Exclusive to the DS version, the Muses are low-ranking deities who aid the Hero.

• Kalliope (カリオペ, Kariope):
• Thaleia (タレイア, Tareia): A butterfly fairy Muse.
• Repsira (レプシラ, Repushira): A centauress Muse.
• Euter (エウテル, Euteru): A cybernetic Muse.
• Leio (レイオー, Reiō): A mermaid Muse.
• Aleito (アレイト, Areito): An east oriental Muse.
• Polynia (ポリニア, Porinia) and Melmene (メルメネ, Merumene): Twin sister Muses, Polynia wears red and has bladed gauntlets while Melmene wears blue and has shield gauntlets.

Final Fantasy Legend II was developed by Square Co. in 1990 under its original Japanese title Sa・Ga2: Hihō Densetsu. The project was headed by Akitoshi Kawazu and Hiromichi Tanaka, who had previously developed the game's predecessor, The Final Fantasy Legend one year earlier. Like its predecessor, Final Fantasy Legend II was designed to be difficult and have advanced gameplay, described by Kawazu as the main difference between the SaGa and Final Fantasy series. The game's music staff consisted of Nobuo Uematsu, famous for his involvement in the Square's Final Fantasy series, and Kenji Ito. In December 1991, the game's music would be released by NTT Publishing on a compilation soundtrack featuring themes from the first three Final Fantasy Legend games called All Sounds of SaGa. The album's popularity would allow it to be reprinted in December 2004.

In November 1991, the game was translated and released in English by Square America, and like its predecessor was renamed Final Fantasy Legend II in order to tie into the popularity of the Final Fantasy brand. Due to the popularity of the game, Sunsoft America Corp. entered into a deal with Square to obtain the publishing rights to a re-release of the three Final Fantasy Legend titles, which were made available in April 1998. Despite advertising the game as being compatible with Nintendo's Game Boy Color handheld, the re-released version featured no enhancements.

Nintendo DS version

In January 2009, Japanese magazine Shōnen Jump announced that SaGa 2 Hihō Densetsu: Goddess of Destiny, a remake of Final Fantasy Legend II for the Nintendo DS, was being developed and directed by Kawazu and would feature fully three-dimensional cel-shaded graphics. In an interview with Famitsu magazine, Kawazu stated that he and his team had been planning a remake of the game ever since they remade The Final Fantasy Legend for the WonderSwan Color in 2002, and went ahead with the project now that they felt "the time was right". Youichi Yoshimoto, who had previously worked on Unlimited Saga, was appointed project supervisor, along with Kenji Ito who arranged the game's soundtrack. Gen Kobayashi, character designer for Square Enix's The World Ends with You, provides the game's new promotional and character artwork.

The remake was produced to add new features but still keep the core story and gameplay of the original, and is designed to retain the Game Boy version's play time of "ten-odd hours" from start to finish, which Kawazu feels is adequate for a handheld role-playing game, stating "This is on a portable system, and for that I think it's better not to have a game you must sit down and play for hours on end, but rather something you can enjoy in small pieces at a time." Unlike the Game Boy version, battles in the Nintendo DS version no longer occur randomly, and were adjusted to be more like later games in the SaGa series where enemies appear on the field screen along with the player and are encountered when touched. Also unlike the original, where a character's stat increases through gaining levels was largely randomized, characters now become stronger in a "less opaque" fashion, with more defined growth tables for each playable character. A new multiplayer boss arena allows up to four players to battle the game's bosses to win various rare items. The game's released in 2009 coincided with the 20th anniversary of the SaGa series, and was made available as part of a limited edition Nintendo DSi bundle.

Game Boy version

As of January 2009, the Game Boy release of Final Fantasy Legend II has sold an estimated 850,000 copies in Japan since its release in December 1990. In March 2006, the title was voted the 94th best game of all time by the readers of Famitsu magazine as part of its "All Time Top 100" poll.

The game was mostly well-received during its release in North America. Nintendo Power declared it to be superior to its predecessor, calling it "longer and more involving than Square Soft's original Game Boy RPG". The magazine also found it to be more user-friendly, stating that it "includes features that will make playing more enjoyable for both RPG enthusiasts and beginners", but found it mostly lacking in play control. During their annual Nintendo Power Awards, Final Fantasy Legend II was nominated for "Most Challenging Game Boy Game" of 1991. In their review of the 1998 re-release, IGN found that the game had aged when compared to more modern role-playing titles and that "gamers jaded with today's FMVs and polygon graphics may find it hard to get drawn into a game with simple sprite characters." Regardless of the game's antiquity, the website still found it to be a solid game with "great character development, a breathtaking score and a solid Role-Playing game engine, there is very little that stands in the way of an RPG gamer and this title," calling it "by far" the best of the Final Fantasy Legend games. The game maintains a 90% average rating on aggregate review website GameRankings based on two reviews.

GameDaily named it alongside the related Game Boy Final Fantasy titles as definitive games for the system, describing it as providing "hours of role-playing excitement, whether you were waiting in a dentist's office or on the way to Grandma's house." The sentiment was shared by gaming magazines Electronic Gaming Monthly and Pocket Games, the latter of which ranked the titles together 8th out of the Top 50 games for the Game Boy.

Nintendo DS version

The Nintendo DS remake received a 31 out of 40 scores from Japanese Weekly Famitsu magazine. The game sold 146,000 copies by October 2009.