Two hundred years after Bartz, Lenna, Galuf, Krile, and Faris saved Planet R from Exdeath, a new evil arrives from the Black Moon, and seeks to take the Crystals. Linaly, a descendant of Bartz, and her friend and protector, Prettz, journey to the Temple Of Wind to seek the source of this new danger, forming a new generation of Light Warriors.

In the year 1000 cosmic calendar of the Kario Yuga era, the planet R, attended by two satellites, is an Earth which enjoys an abundance of majestic nature and a shining blue ocean.

It's existence is maintained by four Crystals which control the four basic elements of the universe: Earth, Water, Fire and Wind.

Once upon a time, when this planet was menaced by a dark entity and faced its biggest crisis the most courageous ones desperately fought to protect the crystals in a battle since long forgotten, but... Introduction

Linaly learns of the disturbance in the crystals' force, and upon this, Linaly and her grandfather, both descendants of Bartz Klauser, embark on a quest to protect the Wind Crystal. Prettz, a boy hailing from the same village as the two, follows despite having been told not to. Their journey leads to a deserted town where they are attacked by a mantis-like monster, whose threat they can only overcome thanks to Prettz's intervention.

As Linaly's grandfather is unable to continue the journey, Prettz takes his place. The pair gets attacked by Rouge and her pirates, but Prettz tricks and defeat them. Using her earring, Linaly asks the spirits of the land for guidance through the Valley of Dragons, beyond which the Wind Shrine lies. Having been told to follow the flow of the wind, Linaly allows herself to be taken away when she and Prettz enter a sandstorm. While she finds the way thanks to her trust in the wind, Prettz is buried with his motorcycle and has to be dug out by Linaly.

The pair makes it to the Wind Shrine, which is floating in a hidden valley. While Prettz goes off to hijack the pirates' airship, Linaly solves an ancient puzzle, bringing her to the shrine's entrance moments before Prettz crashes the airship near it. The pair climbs the Wind Crystal and soon discover that using a motorcycle in the shrine is a bad idea.

The pair reaches the Wind Crystal and obtains it, albeit not exactly the way they intended to: The Wind Crystal decides to hide within Linaly's body leaving her in pain and glowing. Prettz and Linaly exit the Wind Shrine to go to the Blue Mage of Tycoon Castle, so that he may cure Linaly.

The crystals of Earth, Water and Fire have been stolen by the evil forces and Planet R is suffering from many grave disasters. Meanwhile, Prettz and Linaly, a descendant of the legendary valiant ones, must travel to the temple of the Wind to protect the one remaining crystal, overcoming many dangerous obstacles along the way. After finally reaching the Temple of the Wind, the crystal makes an extraordinary move and magically dives straight into Linaly's body... Introduction

Prettz and Linaly are apprehended by the Iron Wings of Tycoon after leaving the Wind Shrine. Due to being under the suspicion of having stolen the Wind Crystal, and being a companion of those who stole the other three, the Iron Wings Commander Valkus asks them to surrender. Prettz denies everything and starts escaping with Linaly. After being shot by Valkus, Prettz engages the commander in battle.

Rouge's pirates emerge and put everyone to sleep. The pirates capture Linaly and Prettz as well as Valkus, hoping to make some profit from them in one way or another. They take them to Rouge Island where Rouge intends to learn the Wind Crystal's hiding place. She orders one of her pirates to torture Prettz, but has no result with this method. When she tries to torture Linaly, Prettz attacks her despite being tied up, before getting knocked out.

Back in their cell, Valkus ponders over his feelings as he has fallen for Rouge, while Linaly is in pain. The Wind Crystal leaves her body and summons the ghost of Mid Previa, one of the courageous ones who assisted the Light Warriors in their battle against Exdeath 200 years ago. Linaly is surprised over meeting a former companion of her ancestor, while Prettz begins to dislike the ghost of the young boy and names him a dirty old man for hiding in a young girl's body.

Mid and Prettz continue to go at each other. Mid apologizes for hiding the crystal within Linaly, but states it was necessary to fool the enemy, Deathgyunos. He hides the crystal within Linaly once more, ignoring protests from Prettz. Rouge returns and takes Linaly away to interrogate her. Prettz snaps Valkus out of his trance and gets him to open an escape path. He storms Rouge's room, knocks out two guards and grabs a sword to go on a rampage before escaping with Linaly. Guided by Mid, they find a storehouse with Prettz's motorcycle and Kiku-ichimonji, which they use to escape.

The Deathgyunos troupes launch an attack, forcing the heroes, Valkus and the pirates to work together. Prettz plays the bait and lures the enemy soldiers away, creating an opening for his allies to flee. He lures them into the storehouse where he sets up the explosives. The ensuing explosion obliterates the island, leaving Prettz's fate in the dark.

Linaly spots a single barrel in the sea and jumps off the airship to swim to his side, overjoyed he is alive. An angered Deathgyunos commander states the failure of his soldiers is unacceptable, and his soldiers assure him they'll capture the girl without fail.

While being imprisoned by the pirates on Rouge Island, Prettz, Linaly and Valkus encountered a ghost boy from 200 years ago who appeared from the Crystal of the Wind and told them about Deathgyunos and their attempt to conquer the universe. Having already won the Crystals of Earth, Water and Fire the enemy attacked them on Rouge Island to try and take the Crystal of the Wind. With Prettz's effort, they barely escaped the crisis and the pirates' Rouge Island dissipated into the ocean... Introduction

The Iron Wings return to Tycoon after the battle on Rouge Island. Having taken the pirates prisoner, the soldiers are proud of themselves, much to the displeasure of both the tied up Rouge and Valkus, who is pained to see his beloved one in chains. A message from Queen Lenna arrives, ordering the soldiers to treat Prettz, Linaly, Mid and Rouge as guests.

Upon arriving at Tycoon Castle Valkus and Queen Lenna's guests meet the queen for an audience, during which the queen labels them as the new Light Warriors. Mid is interrogated and tells his story: Following his grandfather's death, Ra Devil appeared and stole Cid's brain, killing Mid in the process. He reveals Ra Devil's goal is to become Deathgyunos, god of the universe. The party deduces that the Deathgyunos's hideout is located on the Black Moon.

They plan to travel to the moon and recapture the crystals of Fire, Earth and Water by using the Hyriuu, the guardian god of the Tycoon Kingdom. Linaly, Prettz and Mid opt to go through the ancient dungeon below the castle to reach the dragon and awaken it.

While the trio is on its way, Tycoon Castle is attacked by the Deathgyunos forces, and has to depend not only on the Iron Wings, but on the pirates and their airship to withstand the onslaught. Some of the mechanical soldiers slip through the defenses and pursue Linaly's group, leading to Prettz having to fight them. Linaly is captured by the last remaining soldier. Prettz attacks him while riding on his back and the group falls from the bridge they had been crossing.

At the bottom they find the Hyriuu's tower, which has been sealed. After standing on an ancient floor sigil the power of the Wind Crystal residing in Linaly's body is unleashed and she fires a beam of light at the tower, unsealing it. The trio enters the tower and finds a miniature Hyriuu. Disappointed, Prettz laments their bad luck, while Linaly befriends the little dragon. A golem controlled by Ra Devil appears and captures Linaly, leaving Prettz to fight him, albeit with temporary success—after being struck down once, the golem reforms around Linaly's body rendering Prettz unable to attack him, forcing him to let Ra Devil escape with the girl. While Prettz finds Linaly's earring and laments his inability to protect her, the saddened Hyriuu cries out and transforms into a flying dragon. Filled with hope, Prettz swears to free Linaly.

From a confession made by Mid, grandson of the legendary and courageous Cid, the true identity of the plunderer of the Crystals is revealed. Prettz, Linaly, Rouge and Valkus have been asked by Queen Lenna to recover the Crystals of Earth, Water and Fire. With the help of the Flying Dragon, guardian god of Tycoon kingdom, they were determined to venture into the Evil headquarters: The Black Moon. But just as they were about to begin their journey, the enemy made a surprise attack and kidnapped Linaly in whose body the Crystal of Wind temporarily resides... Introduction

Ra Devil is in a bad shape and is only held up by a multitude of machines. He has wandered the universe in search of the truth before finding it in Deathgyunos and says the time has come for him to become Deathgyunos himself, the ruler of the universe.

The four crystals have been placed in a machine where Linaly takes the place of the Wind Crystal due to carrying it inside her. The spheres containing the crystals start glowing and Deathgyunos's reforms itself, opening a solar sail. Several streams of energy converge on the Black Moon and are gathered by the airship and propagated to the machine. Ra Devil announces he can feel the power of the entire universe flowing through him. The power is drawn from the crystals, which awakens Linaly.

The pirates' airship approaches the Black Moon being pulled by the Hyriuu along with the Iron Wing, aboard which Valkus concerns over Ra Devil absorbing energy out of the universe. Ra Devil's body begins rebuilding himself, a feat upon which the imp-like beings on the moon's surface rejoice, stating that their god is about to be born. The Hyriuu along with the two airships enters the Black Moon's atmosphere but the dragon is hit by a lightning bolt and tumbles down, and the airships crash on the Black Moon.

The pirates' ship is heavily damaged, leaving Rouge to order her crew to repair it while she goes to the Iron Wing along with two of her pirates. On the way she catches the unconscious and now once more minuscule Hyriuu as he falls from the sky. She tosses him over to her remaining crew, stating that while fixing the ship, they should fix him too.

Ra Devil's new and still incomplete body rises into the air, while the imps rejoice as Deathgyunos, god of the universe, has been reborn as their master. Using Linaly's earring Prettz tries to mimic her and converse with the spirits. He contacts Mid who tells him to head north. The Iron Wing is engaged by the enemy and the Iron Wings send out their elite troops, but get in the line of fire. Rouge is hit on her shoulder and Valkus turns berserk, shooting at every enemy without hesitation eliminating them on his own, to which Mid only can say that "Love makes one insane."

Deathgyunos is still not fully constructed, but nonetheless opens fire at the Iron Wing and the heroes launch a full-scale attack, colliding the ship with Deathgyunos. Prettz and Valkus split up with Prettz looking for Linaly, and Valkus searching for the crystals in the debris. Prettz encounters a robot carrying Linaly, which opens fire on him before attempting to escape. Prettz catches up and destroys the robot with his Kiku-ichimonji, rescuing Linaly. Linaly attacks Prettz knocking him out, before Mid appears and lifts the mind control off her. After Prettz regains consciousness and learns Linaly was under mind control, he returns her earring to her.

Valkus and his men find the three crystals, and Rouge urges them to leave the Black Moon, but the Iron Wing is unusable. Mid can hear Cid's voice calling out to him and goes to look for it, finding his grandfather's enlarged brain. Mid talks with him, promising to take him home. Deathgyunos starts moving once more, claiming it is the truth of the universe, and as such does not know death. Mid engages Deathgyunos and stalls him, buying his friends time to make their escape, but before they can reach the pirates' airship, Deathgyunos emerges once more.

Valkus and Prettz lure Deathgyunos away from the airship. Linaly and Rouge join them and Linaly starts emitting light from her body just before the Wind Crystal leaves her to make its new home in Prettz. The heroes battle Deathgyunos and Linaly summons a wave of chocobos at him. The onslaught of featherless birds takes Deathgyunos down, but his upper part rises to attack them. His last stand is short lived as Prettz charges and cuts it cleanly into two halves.

Following this victory, Mid reappears, fine and well. He thanks the party for having helped him free his grandfather, before the old Light Warriors appear with Cid holding his brain in the middle. Mid departs alongside his grandfather. Using the chocobos summoned by Linaly, the party returns to the pirates' airship ready to return to Planet R.

Linaly's grandfather is heard complimenting his granddaughter as she has proven herself a true descendant of the courageous Bartz. Hyriuu pulls the pirates' airship back to the planet, and the party, along with Queen Lenna, visit the Wind Shrine, returning the Wind Crystal to its rightful place. Rouge returns to pirating and Valkus joins her crew. Linaly, her grandfather and Prettz continue their journey home.