In the aftermath of a war fought by magnetic weapons which caused massive earthquakes, a young and spunky boy named Conan gets involved in a grand adventure. Conan lives in a world that is mostly oceans; the major land masses having been destroyed by the weapons of the great war. He meets a young girl named Lana, and they eventually foil the plans of the city-state of Industria which wants to regain the lethal weapons.

The year is 2148. Two years after the end of the original Fafner in the Azure TV series, Tatsumiya Island and its surviving residents have returned to some semblance of recovery. However, things have become desperate for our hero, Kazuki; nearly blind now, and partially crippled from his battles with the Festum two years earlier, he clings to the promise his fallen friend Soushi made to him to return to the island and set things right again. Kazuki's hopes flare when a lifeform is detected within an unmanned submarine that comes floating into Tatsumiya Bay one night, but the person aboard isn't Soushi; it is a mysterious "boy" named Misao Kurusu who may not be entirely human, and who claims to have been sent by Sōshi. With Misao's arrival, hostilities break out anew between the Human Army and the Festum, and the Fafner pilots are thrown into the most desperate battle of their lives - this time, with the fate of TWO races riding on their shoulders. 

(Source: Wikipedia)

The film opens with Nefeltari Vivi flying with Pell in a brief flashback. Returning to the present, Vivi and the Straw Hats meet Crocodile's subordinate Mr. 2 Bon Clay. Mr. 2 shows the Straw Hats his devil fruit ability, which allows him to assume the form and voice of anyone whose face he has touched. Vivi describes a brief history on how the Baroque Works leader Crocodile has used Dance Powder while posing as the country's hero. He has also tricked the rebel and royal armies into fighting each other. Once in Alabasta and after crossing the desert, the Straw Hats find the rebel's base deserted, while the rebel army, led by Vivi's childhood friend Koza, witnesses the port town Nanohana being burned by members of Baroque Works disguised as soldiers of the royal army. The rebels decide to attack Alubarna, where at the same time Mr. 2 impersonates the king, Nefeltari Cobra, and orders the royal army to engage. Meanwhile in the desert, the Straw Hats are intercepted by Crocodile and his partner, Ms. All Sunday. Crocodile aims for Vivi, but Luffy stays behind and distracts him, while the other Straw Hats escape. In the ensuing fight, Crocodile defeats Luffy by impaling him through the chest with his hook and buried alive.

The game is set in the continent of Babel, where the Tower of Babel looms large over seven nations. After the invention of alchemy led to its use as a tool of war that brought humanity to the brink of extinction, the seven nations struck an uneasy peace that led to a prohibition on alchemy for hundreds of years since. In the Continental Year 911, the nation of Lustrice broke the pact by assembling an army bolstered by alchemy, with ambitions of conquest over the continent. Led by Envylia, the six nations allied and struck down the rogue nation, casting alchemy once again to darkness. But 20 years after the war, alchemy once again begins to cause chaos in the land. 

(Source: ANN)