Here's a rundown of what basically happens throughout the four chapters of the series. It does not stress all of the character interactions, merely a list of plot elements. I also did not include the many cutscenes of Ra Devil and his robotic minions plotting the horrible destruction of Planet R.
Wind Chapter: Linaly's grandfather senses that there's something wrong with the wind. He decides to go on a journey to the Temple of the Wind, but Linaly insists on accompanying him. Prettz spies them going in their boat and demands to go with them, but Linaly's grandfather doesn't trust him and declines vehemently. Eventually, Prettz follows them in his motorbike until a giant monster overtakes them. Linaly tries Summoning, but all she gets is a Chocobo who runs away. Prettz saves them with his sword, but Linaly's grandfather is stricken and must stay behind. Linaly honors her grandfather's wishes and refuses to ride in Prettz's sidecar - until Rouge's pink airship overtakes them. She demands Prettz's bike and whatever's in it. Prettz replies in usual style - insults - and the pirates attack. Prettz easily subdues them with his homemade explosives and continues on, unaware that he's incurred Rouge's incisive wrath. On the way, Linaly and Prettz get lost in the forest. Linaly's grandfather communicates with her via her Yin-Yang earring. She takes it off and the forest spirit guides them to the Wind Temple. The temple is floating and unreachable. While Prettz sprints off to hijack Rouge's ship, Linaly solves the puzzle of the nearby floor tiles and the tiles become columns which rise up and take Linaly to the entrance. Prettz is nonplussed. The Wind Temple allows them through to the Crystal. Upon touching the Crystal, Linaly gets a vision of the four Valiant Warriors; the Crystal then flies right into Linaly's stomach! In the meanwhile, Valkas and the Iron Wing have arrived, assuming that Linaly and Prettz are temple defilers. (They discover that the other three Crystals have already been taken by Ra Devil.) Linaly and Prettz exit the temple on Prettz's bike, unaware of the ambush waiting for them...
Fire Chapter: Valkas exchanges insults with Prettz, but in the meantime Rouge listens in from her pink ship and finds out about the Wind Crystal. Coveting it, she gasses the whole lot and takes Valkas, Linaly, and Prettz captive. Rouge tries torturing Prettz with a tickle device to get him to tell the whereabouts of the crystal, but he withstands it. Valkas instantly falls in love with Rouge. The ship flies to Rouge Island, where Rouge puts them all in the same cell. After Prettz's futile attempt at bending the bars, the Crystal unexpectedly releases itself from Linaly's body, and the ghost of Mid comes out. Mid tells his story, how he helped the Valiants defeat Exdeath and now Ra Devil and Deathgyunos is trying to destroy the world for reasons unknown. The crystal then reinserts itself in Linaly's body. Rouge then reveals herself, having heard the whole thing. She takes Linaly away. Prettz, overcome by rage, coaxes Valkas to bend the bars, letting him slip through and chase after Linaly. He finds Rouge feeding her prune juice. 8-) He slices up some gold treasures (which really pisses Rouge off) and proceeds to pull off a daring escape on his bike. However, an unexpected attack by Ra Devil's forces makes everyone work together. The Iron Wing finds Valkas again; everyone but Prettz (who's still stuck in Rouge Island) hightail it onto the Iron Wing and Rouge's pink ship is tethered to it; Prettz then finds a room teeming with explosives, throws his own explosive into the place, and ends up sinking the island. However, Prettz manages to hide inside a nearby pot, saving himself from death as the island sinks. Linaly calls her friend Kisana, a sea serpent, to help reach Prettz. The entire party now together on the Iron Wing, they fly for Tycoon. However, by the orders of Tycoon Castle, Rouge is not allowed to go free and is chained to her chair.
Dragon Chapter: Valkas receives transmission from Tycoon allowing Rouge to go free. The party finally reaches Tycoon Castle, where they are met by Queen Lenna and Blue Mage Hassan. Once the entire party is together, Queen Lenna reveals that the Wind Crystal has chosen the four (Linaly, Prettz, Valkas, and Rouge) to fight against Ra Devil. Mid now tells his full story: when his grandfather Cid (who is translated here for some bizarre reason as "Shido") died, he took with him the wisdom of the Crystals; he had all his papers burned. When Mid went to the graveyard to mourn, Ra Devil appeared and took Cid's brain from the body. When Mid cried out, Ra Devil sent a single laser beam through his heart, killing him. However, his soul could not rest while this indignity had been committed to his grandfather. It now comes out that Ra Devil needs all four Crystals to become Deathgyunos, a god-like entity who means total destruction and oblivion. They deduce that Ra Devil's hideout is on the Black Moon, but the only way to reach it is by waking the legendary Hiryuu (Flying Dragon) who rests in the nearby Dragon Tower. However, even as they speak, Ra Devil's robotic forces begin attacking Tycoon. Linaly, Mid, and Prettz continue to the Dragon Tower while everyone else (even Rouge, after being paid a king's ransom by Queen Lenna) fights against the enemy. Two robotic enemies attack en route to the bottom of the Dragon Tower, but Prettz gets both of them (aided by a summoned Chocobo from Linaly). The second one, however, held the red eye of Ra Devil which does not disappear. The bottom of the Dragon Tower is a large lake. Prettz tries swimming it, but then Lenna and Mid uncover a way by land, leaving Prettz half-stranded on a giant stone head. They find the Hiryuu, but it's only a baby. The red eye of Ra Devil suddenly begins attracting stone to itself, becoming a statue-like apparition. Ra Devil speaks to them, but Prettz slashes the stone being to pieces before it can do anything. They take the Hiryuu and try to leave, but the stone re-assembles itself. Linaly is stolen away from Prettz as he watches, and Ra Devil takes her away to the Black Moon. Ra Devil's forces retreat from the attack. The Hiryuu suddenly grows to full size and the heroes prepare to travel to the Black Moon.
Star Chapter: The Hiryuu tows the Iron Wing and Rouge's pink ship towards the Black Moon. However, Ra Devil's forces attack. The Iron Wing is totaled, Rouge's ship is damaged, and the Hiryuu regresses to a baby again, but the Black Moon was reached. Prettz and Valkas head to Ra Devil to rescue Lenna, but it's too late - Ra Devil already transformed into Deathgyunos. There's a longish battle scene and Deathgyunos falls. Prettz finds Lenna but she's not in her right mind - she beats him up. Mid blows on her and she recovers, though. After retreating from a giant green monster, the Crystal suddenly transfers itself to Prettz from Lenna's body. They then discover that Deathgyunos is not dead yet. It takes the firepower of Valkas and Rouge, a barrage of Chocobos from Linaly (her Summon power is augmented by the crystal), and Prettz's samurai sword to the evil red eye to finally destroy it for good. The Crystals are then returned to their rightful places, Mid's soul rests in peace with his grandfather and the other Valiant warriors, Valkas joins Rouge's band of pirates, and Linaly and Prettz head home.