With the four Crystals restored, the Warriors return to Cornelia, only to find the darkness more prevalent than before. They then proceed to defeat the Fiend Kraken and restore the Water Crystal. On the way to the Water Crystal, Neon admits to the Warriors that unlike them, she was born in Cornelia and now remembers that she was given her crystal by Astos. They subsequently find the Earth and Fire Crystals, defeating the respective Fiends Lich and Marilith. As they journey to the Earth Crystal, the Warriors begin to recover fragments of their memories as they defeat monsters and absorb the darkness mist they expel into their crystals, and remember they all come from a faraway land beyond Cornelia. The Wind Crystal is restored and Sophia decides to join the Warriors. They defeat the Fiend of Chaos guarding the Wind Crystal, Tiamat, who reverts to another defeated hero named Sophia. While searching for the Wind Crystal, the Warriors are transported to the Flying Fortress, a space station orbiting the planet. To find the crystals, the Warriors meet with Astos, the King of the Dark Elves, who points them in the direction of the Wind Crystal. The King then tasks the Warriors with restoring the Crystals of Wind, Fire, Earth, and Water to save the world. As they return to Cornelia, they muse about how all four of them have lost their memories, and Jack reasons it's to prevent them from making personal attachments that could interfere with their duty. Neon decides to accompany Jack's party as the fourth Warrior of Light. Jack is skeptical of her story, and maintains that Chaos does exist and he will find it. She had originally planned to absorb all the world's darkness to become the singular entity of Chaos that could be defeated by a band of heroes, but failed.

She explains that she had also sought out to destroy Chaos ten years ago, but realized that Chaos is simply a myth created by humans to rationalize the existence of darkness.

Jack and his party enter the Shrine of Chaos and seemingly defeat Chaos, only to reveal that the person they fought is a young girl named Neon, who similarly possesses a black crystal like them. While the King and his court are skeptical of Jack, Ash and Jed being the prophesied Warriors of Light due to the fact they are a party of three instead of four and possess only black crystals, the King allows them access to the Shrine of Chaos. They petition the King of Cornelia to allow them to enter the Shrine of Chaos and destroy Chaos itself. Jack arrives in the kingdom of Cornelia, intent on destroying Chaos whose darkness has begun to plague the world, and is quickly joined by two other warriors, Ash and Jed, who have a similar mission. During the journey they face a knight who has taken on the role of Chaos while seemingly the foretold Warriors of Light, each has doubts as to whether that is their role. Jack is accompanied by other companions, including newcomers Ash and Jed. The main character is Jack, a man consumed by a need to destroy Chaos. Stranger of Paradise is set in a dark fantasy interpretation of the setting for the original Final Fantasy game.

Once an enemy's 'break gauge' is depleted, Jack can perform a finishing blow that crystallizes the enemy, allowing Jack to harvest them and restore a portion of his magic meter. Combat takes place in real-time, with Jack being able to switch between two assigned jobs and use physical and magical attacks. Stranger of Paradise: Final Fantasy Origin is an action role-playing game in which players take on the role of protagonist Jack, exploring environments and fighting monsters of the Final Fantasy series.

Final fantasy origin