- Ryu - After being awakened from his slumber, Ryu, in his dragon form, goes on a rampage in the Dauna Mines. He is captured and while being transported, escapes into the forest below the railway line. Ryu reverts to his human form, and is befriended by two mischievous orphans. As the three friends become closer, tragedy separates them and Ryu's quest to find his friends begins.
- Teepo - A purple-haired orphan found by Rei an undisclosed period of time before the thief found Ryu. Teepo is a classic punk; he despises authority and loves to lash against it, though he craves attention as well. Despite his gruff attitude, he cares deeply for his adopted brothers Rei and Ryu, and losing them would severely scar him emotionally. As disclosed near the end of the game, Teepo was also a member of the Brood, and a fellow Clansman to Ryu; but unlike Ryu, he agreed with Myria's assessment that the Brood were far too powerful to be left to their own devices and allowed himself to be imprisoned in Eden for eternity. He attempted to turn Ryu to his side, but in the end failed. Slain by his comrades, his last words were that he only wanted the life he, Rei and Ryu had all those years ago back.
- Rei - A thief of the Yrall Region, Rei is one of the last remaining members of the powerful Woren Tribe, a race of powerful humanoid tigers with exceptional agility and physical capabilities. Rei himself is possessed with the ability to transform into the deadly Weretiger, a vicious, powerful, though berserk version of himself; were it not for the power of the Brood, his race may have been extremely dominant. Very little is known about Rei's past, though it is likely he was an orphan like Teepo and Ryu. He acts as an elder brother to the two Brood children, and as such is extremely protective of them, becoming vengeful and bitter when he believes them to have been killed by a powerful crime syndicate. After the three are attacked by the Horse Brothers Balio and Sunder, Rei vows revenge upon the syndicate that disrupted their quiet little life, and goes on a hunt for his attackers and those who hired them. After a killing spree in Syn City and killing the syndicate's leader Mikba, he joins Ryu's group again to see if God can answer why people like him are born with the powers they have.
- Nina - The offensive magic caster of the group, Nina meets Ryu as a child, taking pity on him and freeing him from prison. Years later, their paths cross again as young adults.
- Momo - A reclusive scientist who holed herself up in a great tower after her father's death in order to try to finish his incomplete research on the magical ore known as chrysm. A red-haired, long-eared young woman, she is possessed of a natural genius probably inherited from her father. This intelligence comes with an unintentional arrogance that she exhibits by making claims that her father's research (and therefore some of her own) is great and probably infallible. Despite this, however, she is a kind-hearted individual whose curiosity and intelligence drive her to finding new ways for science to benefit the world. In the game's second half, Momo follows Ryu and his friends to discover the origin of the machines that wash up on the shores of the Eastern World. She has a cameo in Breath of Fire IV.
- Peco - A curious little talking onion created from the charred remains of a genetic mutation, Peco serves as the comic relief of the Breath of Fire crew. Though his importance to the story is primarily innocuous at first, he serves a far greater purpose as the game moves on. He is one of the last of the Grassmen Tribe, and a voice of the ancient Tree of Wisdom, Yggdrasil. Through him, Yggdrasil exerts his influence to counter some of the damage Myria has done, and is seen returning life to the barren Desert of Death.
- Garr - The longstanding Champion of the Tournament of Champions, Garr is one of the Four Guardians created by Myria, the Goddess of Destruction, to eliminate the Brood from the face of the Earth. He, along with his brethren Guardians Gatz, Gaw and Gaist, slaughter the Brood who put up no real resistance. He frees Ryu from the clutches of Balio and Sunder, in order to take him to Angel Tower, and execute him, the last of the Brood. But Ryu defeats him handily, which Garr anticipated, bringing to light the guilt and doubt that he had bottled up within him for centuries since the war's end. He knew the Brood could have eradicated him and the other Guardians had they wished, yet they allowed themselves to be destroyed. In the game's second half, Garr finds Ryu in hiding to beg his forgiveness, and takes him to see Myria, to ask why the Brood needed to be killed.
- Myria - Returning from the original Breath of Fire as the main antagonist of the game, she acts as an overzealous mother to all the world's creatures, "protecting" them from the potential dangers of technology and the Brood (the nigh-extinct dragon clan of the game). This however, turns out to be her downfall as she is bested by the only remaining member of the Brood, Ryu.
Set in a fantasy world, the story concerns Ryu, a young boy with the mysterious ability to transform into powerful dragons, who must discover the truth behind his origins, as well as locate his lost friends and surrogate family. The game's plot is presented in two parts: the first half concerning Ryu as a child, and the second half as an adult. He is accompanied by a number of supporting characters who aid him on a journey that leads them across the world, eventually confronting a mad goddess.
The game begins in a chrysm mine in a far corner of the world, where a rare and powerful mineral is being harvested from the fossilized remains of dragons. When a large deposit is cracked open by dynamite, a preserved baby dragon emerges and quickly attacks the panicked miners before being knocked unconscious and placed aboard a train to be taken away for study. On the way out of the mine, the dragon jostles his cage off the train and falls down a hill on the outskirts of a large forest, where he transforms into a young boy before again losing consciousness. He is found by a wandering thief named Rei, member of the cat-like Woren clan and fellow orphan who believes him to be just another abandoned child. Taking him to his home in the woods, they meet Teepo, Rei's longtime friend and partner-in-crime, who agrees to let the boy into their thieving operation, and find out that his name is Ryu, the only thing he can remember. The team commits several crimes, and come into favor with local villagers when they steal from their corrupt mayor, McNeil, and re-distribute the funds across town. Secretly a member of a large crime syndicate, the mayor contacts two hitmen, the horse brothers Balio and Sunder, to seek revenge, who proceed to burn down the trio's home and violently attack them. Awakening a short while later, Ryu finds himself in the care of a woodsman named Bunyan who had found no trace of his friends. Believing them to be alive, Ryu travels to the city of Wyndia where he meets Nina, daughter of the King, who helps him escape Balio and Sunder, who are now on his trail.
Ryu and Nina eventually come across a large tower and meet Momo, an inventor and engineer who is researching the properties of chrysm when the two of them arrive. Together with her diminutive robotic assistance Honey, the three escape the tower by rocket when a group of bounty hunters arrive looking for them. Momo leads them to a nearby chrysm research facility conducting experiments on plants when they are approached by the institute's chairman and colleague of Momo's father, Dr. Platt, who tells them that there is a mutant creature causing trouble at the dump area where their biological waste is stored. After defeating the mutant plant creature, it gives up its offspring, whom Nina names Peco, to be cared for in its absence. As the four continue their journey east, where they are captured by Balio and Sunder in a double-cross and taken to a nearby colosseum. It is there that the team meets Garr, a seasoned warrior who aids them in defeating the horse brothers for good.
Garr agrees to help the group in finding Ryu's friends on the condition that he also accompany him to a sacred temple far to the east. After crossing a large bridge and traveling straight through a volcano, the group arrives at the temple, where Garr and Ryu journey inward alone. It is there that Garr reveals the true fate of the Brood, having been slaughtered by him and his fellow guardians by the hundreds at the behest of Myria, an ancient goddess who promised an age of peace in return for their services. With Ryu as the last living dragon, Garr attempts to slay him, only to have Ryu assume his most powerful form, Kaiser, and escape.
Several years later, reports of a rampaging dragon have led Garr to the same mines where Ryu was originally found, and he finds an adult Ryu within its depths. Convincing Ryu that he will not harm him, Garr instead asks forgiveness for his actions against his people centuries ago and asks that Ryu help him discover the truth behind Myria's genocide of the Brood. The two re-group with Nina, now a young adult, and Momo, who has been performing experiments at the plant institute with Peco, who himself has been frequently visiting the great tree Yggdrasil, overseer of the world's forests. They continue their journey once they receive information about Myria's whereabout from Deis, sister of Myria. The team finds Rei alive, now battling the leader of the crime organization responsible for the attack on his friends, and have him join their group, learning that he also has not seen Teepo since the incident. Crossing the ocean to the forgotten northern continent, the group finds a town littered with advanced technology from a forgotten age, and then proceed to the last known village of the Brood, Dragnier, where they learn of the battle between the heroes from the first Breath of Fire and the Goddess centuries ago, and how she has returned to seek her revenge against the Brood. Crossing a large desert, the team arrives at the ruined city of Caer Xhan, a former haven of technology, with a lift leading to Myria's fortress.
Making their way up the large escalator to the floating Myria Station, the group fights their way into the facility's inner sanctum where they meet a lavender-haired young man who reveals himself to be Teepo. Having survived the attack by Balio and Sunder due to his latent dragon powers, he was later contacted by the Goddess, who convinced him to live in peaceful seclusion in her fortress to spare the world his destructive power. Unable to convince Ryu or his friends to do the same, he transforms into the gigantic Dragon Lord and attacks them, only to be defeated, his dying words revealing that he just wanted to be with his "family", Ryu and Rei. The determined group makes their way to Myria herself within the station's control center, where she reveals that she exterminated the dragons centuries ago for the same reason she removed the world's high technology: to keep humanity from inadvertently destroying themselves. She presents Ryu the same choice she gave Teepo: to live the rest of his life in peace within her station, or be destroyed. The spirit of the great tree Yggdrasil then channels himself through Peco and tells her she is taking her power too far, and like any parent, she must allow her children to make their own way. With that, Ryu and his friends attack and defeat her, fleeing the station as it crumbles around them. Garr opts to stay behind to atone for his past mistakes. Ryu and the rest then make their way from the rubble and back into the desert on their journey home.
Breath of Fire III was developed by Capcom Production Studio 3 in 1997, and was the first game in the series to feature three-dimensional environments along with traditional hand-drawn two-dimensional characters.
Series writer and director Makoto Ikehara returned as head of the project, and was joined by a brand new art and sound team that would help expand the ongoing story of the Breath of Fire franchise. The project went through a lengthy development phase with numerous delays, mostly due to several writing and design changes mid-progress. Character artist Tatsuya Yoshikawa went through numerous preliminary designs for each character, only settling on a finalized set of drawings after many character sprites and portraits were already completed. As a result, some character's in-game appearances differ from official promotional material, such as child Ryu having a different hairstyle and wardrobe than his final design.