- The Dark King and his cronies take over Focus Tower (which splits the world into four parts, one for each element) and capture the five Crystals (one for each element, plus Light). The Dark King turns the upper floors of Focus Tower into Doom Castle. The elements begin to decay. The Light Element takes on the form of an old man and meets a boy named Benjamin on the Hill of Destiny. He tells him that he must restore the Crystals and defeat the monsters to restore peace to the world.
- Benjamin enters Level Forest and helps a man get back to his home town of Foresta. The man tells him the trees are dying, and gives him a sample Tree Wither for proof. Unfortunately, Benjamin can't get past Level Forest without an axe.
- He heads to Foresta, where he finds everything withered and old, even the people. Kaeli, a girl from Foresta, conveniently has an axe, and when shown the Tree Wither, agrees to help Benjamin.
- They reach the end of Level Forest and fight a Minotaur, who poisons Kaeli before he dies. Kaeli gives Benjamin her axe, and he takes her back to Foresta to rest up. He begins searching for the Elixir needed to cure Kaeli.
- He comes to the Sand Temple, but the Elixir has already been taken by a treasure hunter named Tristam. He offers to sell it for an insane amount of money, which Benjamin doesn't have. Instead, he offers him a deal: he'll give him the Elixir if Benjamin helps him enter the Bone Dungeon and retrieve the treasure there.
- At the end of the Bone Dungeon, Benjamin finds the Flamerus Rex; when it is defeated, the Earth Crystal revives. Benjamin finds the Sand Coin, a key for the Focus Tower. Tristam discovers his treasure, the Dragon Claw, and gives Benjamin the Elixir.
- Benjamin heads back to Foresta and heals Kaeli, then travels to the Focus Tower. The Sand Coin allows him to enter the water section of the world.
- He meets a girl named Phoebe in the Libra Temple. She tells him that everything is frozen in Aquaria, and she's looking for a spring called Wakewater to thaw it. To do so she needs to travel to the Life Temple, and to do *that* she needs the Libra Crest to transport there. The Crest has been stolen by a giant squid and taken to the Wintry Cave.
- Benjamin and Phoebe retrieve the Crest and travel to the Life Temple to find that most of the Wakewater has dried up. The Light Crystal (still disguised) gives them the small amount that's left over. They try to thaw out Aquaria, but it just isn't enough to work. They decide that restoring the Water Crystal is the only way out.
- They head past the Falls Basin and into the Ice Pyramid, where they defeat the Ice Golem and revive the Water Crystal. Benjamin finds the River Coin. Phoebe returns to Aquaria. She tells him of her grandfather Spencer, living in the river canyon beneath her house. Benjamin meets him and is given a key to a treasure (a Venus Shield) in the Focus Tower. He finds it, meets the Light Crystal again (who tells him to seek out Reuben) and goes ahead to the fire region.
- Earthquakes afflict Fireburg and its environs. One has trapped Reuben's father, Arion, in the nearby mine. They need a Mega Grenade to dislodge the rock trapping him, but the only man who has it has locked himself in his hut. They meet up with Tristam in the pub, who gives them a Multi-Key which allows them to open the door and get the Mega Grenade.
- They dislodge the rock. Arion, though hurt, returns to Fireburg to recover. He tells them that the Fire Crystal is in the Lava Dome. Reuben helps Benjamin get through the Volcano and Lava Dome to defeat the Dualhead Hydra who guards the Fire Crystal. It is revived, and Benjamin gets the Sun Coin. Reuben stays with him as he travels to the wind region past the Focus Tower once more.
- They pass through a rope bridge, but an attack by a monster knocks Reuben to a platform far below, stuck. Tristam enters at that moment and decides to stick around Benjamin some more. Reuben eventually makes it out of there himself.
- They head east to the Alive Forest, where a living tree doesn't particularly like them. Benjamin realizes that Kaeli from Foresta could probably help, and he travels back there to find she's in Aquaria now.
- In Aquaria, Phoebe tells Benjamin that Spencer wants to talk to him. He and Tristam head there. Tristam goes off with Spencer to find treasure, but gives Benjamin his Dragon Claw first. Phoebe comes in to find Spencer and accidentally destroys part of the cavern wall, sealing it off. Benjamin goes back upstairs, gets Kaeli, and returns to the Alive Forest.
- The Giant Tree tells Kaelia that if she destroys the monsters inside it, it'll take her to Windia. She agrees, and she and Benjamin get rid of the Gidrah leading the monsters inside the tree. True to its word, it drops them off near Windia.
- They meet with Otto, a professor in Windia, who tells them that the wind has stopped lately. He also says that his daughter Norma went to Pazuzu's Tower and was trapped there. However, now he can't reach the tower because the wind-powered Rainbow Bridge leading there is down. They must restore the wind; he's sure the cause of the wind stopping is the nearby Mount Gale.
- Benjamin and Kaeli defeat the Dullahan at the center of Mount Gale and restore the wind. Otto rebuilds the Rainbow Bridge. They head to Pazuzu's Tower, rescue Norma, and continue up to defeat Pazuzu, restore the Wind Crystal, and find the Sky Coin.
- Now they need to head to the Doom Castle, but the only way in is by sea. First Benjamin goes to Windia and meets up with Reuben, who takes Kaeli's place in traveling with him. Captain Mac (Kaeli's father) has a ship nearby, but can only be reached by using the Mobius Crest to teleport there. But the crest is in Spencer's Cave, which is blocked off! There's another entrance, but to get there the Rainbow Bridge must be lengthened. To do so, a Thunder Rock is needed. Reuben's father Arion has one, so they travel to Fireburg, get it, and bring it back to Windia.
- The bridge is lengthened, and they return to Spencer's Place. However, Spencer doesn't want to give them the crest. They return to Windia, and Kaeli gives them Mac's Captain Cap to show Spencer. They do so, and Spencer shows them the way to the crest. They use it to reach the ship, which has been overrun by monsters. They destroy them and find Mac. Kaeli shows up and takes him back to Windia.
- Phoebe arrives in Windia and joins Benjamin for the last time in his trek to Doom Castle. He takes the ship there and confronts four palette-swapped versions of the four Crystal guardians, then defeats the Dark King (who's actually a huge spider). The Light Crystal is restored and reveals itself as the old man who helped Benjamin along his way.
- Benjamin goes back to Windia and decides to take Captain Mac's ship to sail around the world. He says goodbye to everyone, but before he leaves Tristam shows up and decides to go along with him. Exeunt Omnes.
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