The story opens with a young Silvite woman named Fina sailing through the night skies in her tiny Silver airship. Not far behind her, Valuan Admiral Alfonso is in hot pursuit under orders from Lord Galcian to capture her. Alfonso opens fire on and disables Fina's ship long enough to capture her before it plummets into Deep Sky, but just as she is being brought onboard his warship, a Blue Rogue vessel arrives with the intent of robbing the Valuan vessel. Vyse and Aika of the Blue Rogues jump from the Albatross onto Alfonso's flagship and fight their way to the rear cargo hold, prompting Alfonso to flee on a lifeboat while leaving Fina behind along with the war beast Antonio that Alfonso set upon the Rouges who quickly defeat it. Vyse and Aika bring Fina back to their clan's ship, which Vyse pilots back to their secret hideout, Pirate Island (disguised as Windmill Island).
While watching the sunset, Vyse and Aika see a Moonstone fall from the skies onto nearby Shrine Island. The next day they travel to Shrine Island to retrieve the Moonstone, a concentrated form of airship fuel, leaving Fina behind in the care of their clan. The Moonstone in hand, Vyse and Aika return to Pirate Island to find it obliterated by the Valuan Armada. Fina and many Blue Rogues have been captured by the Armada and taken to the capital city, and here the game proper begins. What starts as a simple rescue mission becomes a struggle for survival amid a looming world war.
Shortly after leaving Pirate Island, Vyse and Aika are shipwrecked by the legendary arcwhale Rhaknam. They are rescued by a callous but good-hearted fisherman named Drachma, who is hunting Rhaknam. They manage to convince Drachma to take them to Valua City and rescue their friends from death row, luring him with the prospect of a powerful whaling harpoon that is to be found in Valua. Upon rescuing their friends and making a miraculous escape from the Grand Fortress (a history-making feat), the Blue Rogues return to Pirate Island, where Fina admits the real reason that the Empire would go to such trouble to capture her.
Fina's mission is to travel Arcadia in search of the Six Moon Crystals, rare sources of power which can be used to summon organic weapons called the Gigas. The Armada also seeks these weapons with the plan of world domination, and Fina has to find them first. Fina recruits Vyse and Aika to her cause and joins the party, and together with Drachma, fellow pirate Gilder, and frustrated Valuan Prince Enrique, the trio find themselves fighting the Armada and the Gigas at every turn, all the while enduring shipwreaks, betrayal, enemy pirates, and a second capture and escape from the Valuan Grand Fortress. Upon the second escape from the Grand Fortress, Prince Enrique allows Vyse to command the Flagship built for him, the Delphinus, which lets Vyse captain his own airship. They ultimately gather five of the six Crystals and return to Vyse's home base on Crescent Isle, expecting to celebrate and throw a farewell party for Fina, as Fina admits that her elders are in possession of the last crystal, the Silver Crystal.
Instead the party is ambushed by Ramirez, a corrupted Silvite warrior and childhood friend of Fina. Originally sent by his people to live among the Arcadians and observe their behavior, he is disgusted with the greed and conceit of the world (primarily Valua's Upper City); Ramirez now serves the Armada and Galcian whom he believes to be the only person not tainted by greed and corruption and whom he sees fit to rule the world. Vyse, Aika, and Fina engage Ramirez in battle but are utterly defeated. Ramirez reveals that the Silvite Elders were the ones who ordered the Rains of Destruction, a hail of moonstones that ravaged the old world to quell the ancient wars, and both Ramirez and Fina were sent to recover the Crystals so that the Elders may once again call down the Rains. Ramirez also reveals that every Silvite is born with a Silver Crystal in them, and attempts to kill Fina to take hers, but is interrupted by Gilder's timely arrival and retreats.
In order to prevent Galcian from obtaining the Silver Crystal, Vyse and his allies recover the ship Fina arrived in from Deep Sky, the surface of the world beneath the clouds where atmospheric pressure is extreme. They recover and repair the ship, then use it to travel far above the clouds to the Great Silver Shrine, where Fina warns her Elders of Ramirez's betrayal, and lectures the Elders on the trust of people, and the wrongful nature of judging and killing them. Ramirez arrives with Galcian and murders the head Elder and takes his crystal and quickly makes a getaway. Ramirez takes all six Crystals and uses them to activate the continent of Soltis, of which Shrine Island is a small part. Ramirez alone can use the true power of the Crystals: when brought together with the Silver Gigas, they can call the Rains of Destruction upon any or all of the world's six continents, leading to apocalypse. Wishing to be rid of the Valuan Empire which no longer served his purposes, Galcian orders the Yellow Moon to rain on Valua's capital, killing most of the citizens, including Empress Teodora and First Admiral Alfonso.
Ramirez's initial plan is to support Galcian's bid to rule the world. Galcian fights Vyse's fleet of ragtag pirates in the massive Battle of Soltis including directly confronting Vyse and party in hand to hand combat after his fleet and Hydra battlestation are defeated. After escaping the Rogues however, Galcian is killed at the hands of Fourth Admiral Belleza, who sacrifices her life and Flagship to destroy his escape pod in vengenance for his act of heartless destruction of her nation. Ramirez, enraged by what he considers to be Galcian's murder and the death of the only man fit to lead Arcadia, decides to destroy the world. He is undermined by his own former Silvite Elders, who sacrifice their lives to break through Soltis' defensive shield to atone for their judgmental behavior, allowing Vyse's crew entry into the city to confront Ramirez.
Vyse and his party find Ramirez and fight him to a standstill. Backed into a corner and in desperation, Ramirez allows himself to be absorbed by the Silver Gigas, sacrificing his individuality for extra power and a chance at revenge. The Gigas is defeated by Vyse in a ship battle and its core, an amalgamation of the Gigas and Ramirez, falls onto the Delphinus's deck for a final duel. The entity is defeated, and Ramirez and the means of summoning the Rains of Destruction are both destroyed forever. Vyse symbolically "buries" Ramirez's "remains," the Silver Crystal, at sea, and a lengthy celebration follows, after which Vyse, Aika and Fina (now a full-fledged Air Pirate) shed their combative past and return to being full-time Blue Rogues as the credits roll.
Storyline text from Wikipedia.org