You play the role of Bowie, a young school boy, who is tutored by the wise old Sir Astral. Bowie and his friends become caught up in the story when Astral is summoned urgently to the castle, and they sneak in after him.
The young friends and their teacher end up at the Ancient Tower, which has surprisingly opened up. Inside they face their first battle, against a horde of gizmos, one of which escapes at the end to possess the King of Granseal. Using his magic, Astral cures the King, but is himself injured. While sleeping it off, Astral mumbles something about "Ground Seal", which prompts the King to send Bowie and his friends to talk to an old mage named Hawel.
The Force sets off to find Hawel, and on the way encounters his young student, Kazin. They head off together to meet Hawel (from Final Conflict!), and find him surrounded by soldiers and close to death. The soldiers flee, and with his final breaths, Hawel explains that the Ground Seal contains an ancient devil, and is shocked to hear that it has opened. The soldiers came from Galam and took his notes about the Ground Seal. With Hawel's passing, much mystery remains, but it seems clear that Galam is up to no good.
On leaving Hawel's house, the Force are captured by Lemon and the Galam army. They are taken to Galam Jail where they later meet Slade, the thief who started the whole affair by stealing the two jewels. After escaping and battling their way through the castle, Bowie and the Force retreive the Jewel of Light, but are too late to prevent the Galam Army leaving to attack their home town of Granseal.
They return to their invaded homeland to find the mad King Galam is trying to kidnap the Princess! In a brave attempt to stop the abduction, Bowie gains the Jewel of Evil. Sadly, Galam gets away with the Princess, and shortly after this an earthquake begins which forces all residents to flee Granseal in a boat.
When they reach dry land, they find themselves on the continent of Parmecia, in an uninhabited area. They begin to build New Granseal, using the wood from the boat. The King summons Bowie and the Force, and gives them orders to find Princess Elis. A strange bird creature finds its way to the town, and causes a stir amongst the residents. He turns out to be a phoenix by the name of Peter, and he accompanies the Force as they leave the town to look for trading partners and allies.
After visiting a local town, they begin the journey to visit the God Volcanon, and make their way through the Cavern of Darkess to reach Polca Village where a young, blind boy stumbles down from the mountainside. He seems to have come from the town of birdman, Bedoe, and on arrival there they find it has been attacked by Devils. The Force meet God Volcanon, who explains a little about Zeon to them, and goes on to say that he won't help ground-dwellers, as they were the ones who caused the problem in the first place.
They realise they must find their way back to Grans Island to stop Zeon and find the princess, and so, taking the blind boy (Oddler) with them, they travel around Parmecia, looking for a way to return. They run across an old man who knows of an ancient, magical way back - however, when he takes them to the entrance to the magic tunnel, it seems his grandson has locked the entrance from the other side, and the tunnel can't be used.
So, the Force continue their travels, and make their way down a river to the port town of Hassan, stopping briefly on the way to defeat the local sea monster, the Kraken. In Hassan, they discover that an ancient vehicle may be able to help them. They question the local historian, Rohde, about it, but he is too busy to talk to them. To get his interest, the Force return to the town of Ribble to search it's buried ruins for something old - they find the Achilles Sword.
Returning to Hassan with the sword, the Force manage to interest Rohde, and he travels with them to a shrine, where a metal giant guards the Caravan, a vehicle of the ancients. With the Achilles Sword in hand, Bowie defeats the guardian, and Rohde learns how to drive the miniature Caravan. The Caravan can hold many passengers, as everything inside becomes miniturised.
Traveling in the Caravan, the Force make their way along the dried-up riverbed to visit a retired devil, Creed. On their way to his mansion, the Force go through a village of elves, and a cave where some dwarves are trying to tunnel through to Grans.
At Creeds, the Force accidentally stumble upon the devil's "collection" - miniturised people, living in a Desktop Kingdom. The Force are, of course, miniturised too, but after escaping, Creed helps them by taking them to see Evil Spirit. Evil Spirit tells them more about Zeon, at which point Zeon takes over the transmission and tells Bowie to come and visit soon, with the Jewels.
They leave Creed's, even more intent on defeating Zeon, but Oddler remains behind. After briefly returning to New Granseal to report back to the King, the Force travel on to North Parmecia, following the trail of the devil army.
As they head north, a drought is causing problems for Pacalon, a city of centaurs. It's rumoured that something has happened to the Goddess, Mitula, and so the Force take a detour to visit the Goddess. On the way, they meet up with another devil, Cameela, who tries to delay them, without much success. They make it to Mitula's town of Tristan, and make their way to her Shrine. Outside the shrine, they hear voices from inside, talking about a "Lord Oddeye", Astral thinks the name is familiar, but can't quite put his finger on it. So, they enter the Shrine...
Inside, they find Mitula has been trapped by the devil Zalbard. They defeat the devil and his minions, and Mitula is freed. She explains a little more, as do the storytelling statues in her shrine. With the Goddess safe and well, the Force go back down to Pacalon, where there has finally been some rain. Frayja, a vicar, is feeling very guilty because he locked the gate of a town above Pacalon, to prevent the devils getting any further. Afraid that the residents are all dead because of his actions, he tags along with the Force who continue north.
The gates of Moun are still locked when they arrive, and when they enter, they find devils are in the town. Once they've defeated the devils, the Force discover that the residents had taken to living underground, to hide from the devils, so all is well.
The ancient robot, Zynk, suggests you use the Nazca Ship to return to Grans Island, and he leads the way. Cameela once again tries to delay the Force, but is beaten and leaves you with the Sky Orb. The ship is nowhere to be seen - until you look at the ground. There are markings in the shape of a bird, and Zynk explains that this is the Nazca Ship! Entering through it's eye, Zynk uses the Sky Orb to pilot the ship, which carries Bowie and the Force back to Grans. As good as his flying skills are, Zynk's landings leave a lot to be desired, and the ship crash lands in the north east of Grans Island.
Traveling around the north of the island, the Force are able to unlock the door of the magic tunnel, and travel between Grans and Parmecia easily. They pop back to visit Creed, and find that Oddler went crazy, tearing the mansion apart. Creed, apparently, fell into the ocean, and hasn't been seen since.
Back on Grans, the Force encounter Geshp, another devil. He's got some ancient Prism Flowers, which fire lasers, to try to knock down the Force. He fails, of course.
The Force once again continue their journey, and make their way towards the Ancient Tower and Granseal. On the way, they find themselves in a dwarven town - the dwarves they met on the way to Creed's made it back to Grans too!
At various points, they hear rumours of Lemon going crazy, and when they get to Galam, they find he has been trying to take his own life, as a way of making up for all the lives he had taken while possessed. The Force run into Lemon himself at Yeel, but lose him. Astral explains that Lemon has become an immortal, and won't be able to die. The Force then move down to the ruins seen at the start of the game, to retreive the Holy Sword by using the two Jewels. Going back to Granseal, they find in it's place a statue of a devil's head. At this point, Lemon has realised he can't die, and so decides to fight on the side of good instead. Using the Holy Sword at the statue, the mouth opens up and the Force are able to get inside.
Inside, they find a maze, which leads them to a battle against Lord Oddeye - he looks somewhat familiar, and it's then that they make the connection - Oddler was Oddeye. Regretably, they have to defeat their old friend, in order to ascend the tower. At the top, they find Creed, alive and well, ready to help them out in their time of need.
At the top of the tower, Zeon is awakening, and the mad King Galam is there to help the devil king. The Force fight their way past Galam, and then must face the challenge of the devil king himself. With his powers not yet fully replenished, Zeon is beaten, and all seems to be well. Until, that is, Zeon posseses King Galam, and poisons the princess!
Lemon can't bare to see his King being used like that, and tries to stop him. They fight, and the pair of them fall through the doorway to the other dimension. Mitula then appears to reclaim the Jewels from Bowie, and use them to seal Zeon away forever. She can't do it alone, however, and so Volcanon's powers are used to help. The Force wonder why Volcanon would help, when he had forsaken the ground-dwellers, and Mitula explains that it was just a bluff so tha the devils would not rush to revive Zeon if Volcanon was visibly helping.
The princess is still in a bad way, but Mitula explains that she's in a coma. When the poison is purged, she says, the princess' cheeks will turn pink, and it is then that she must be kissed by her true love to awaken her. This could take days, or it could take years.
When the day arrives, it is decided that Bowie should be the one to kiss the princess, even though Jaha makes it clear that he loves Elis. Slade comforts Jaha and tells him that a human should be with a human, not a dwarf. When Bowie goes to do the deed, Sarah becomes upset - it seems that she's been in love with Bowie all this time! - Kazin follows her, to comfort her.
Bowie makes his way up the stairs, to the princess' bedroom. She's lying in her bed, waiting to be woken by his kiss. We are left with a picture of them kissing, and then the credits roll.