Jusqua arrives in Urbeth with a cat he believes is a cursed Princess Aire, in hopes that the local sorcerer can dispel it (the real Aire, however, is elsewhere). After seeking work from the Merchant Lords around the city, Jusqua earns 10,000 gil to pay the sorcerer, and the cat is turned in for the night. Jusqua runs into Yunita and convinces her to help him save the princess.
In the middle of the night the city is attacked by monsters transformed from various dolls the sorcerer had given to the citizens. Jusqua and Yunita clean up the city, but amid the chaos the sorcerer escapes taking the cat with him. Thauzand thanks them and readies a ship to sail to the north to pursue the sorcerer. Jusqua feels it is his responsibility to rescue Aire, and not wanting to involve the princess's bodyguard any further, he leaves Yunita in the night and sails alone to Invidia.
When Yunita learns she has been abandoned she sets out to solve matters on her own. Taking Thauzand's advice, and after acquiring a pair of Rainbow Boots, she travels up the Tower to the Sky and arrives at Spelvia hovering above Urbeth.
Following events in Spelvia, the darkness in Rolan's soul is released and spreads out into the world. After the party is sent back in time, they discover Urbeth was once a city of faith, the four Merchant Lords were the four Priests, and the people are under a plague sent by Beelzebub. The only known cure is the Hi-Elixir, a type of medicine owned by an apothecary who charges a high price for it and the citizens who cannot afford the medicine pray to the gods for salvation. The heroes discover Thauzand's daughter, Elith, is infected with the plague and try to buy a Hi-Elixir from the apothecary merchant to heal her, but he says he has run out of stock and needs to fetch more flasks from the dangerous Hunting Caves. The party journeys into the Hunting Caves and recovers a flask of the Hi-Elixir, which they give to Elith.
The next day, they return to Thauzand's residence to discover his daughter hadn't been cured. She says that "the goddess is weeping", which prompts Thauzand to climb the Tower of the Sky to pray alongside the other priests, as they haven't prayed in some time. The party follows him to the Tower of the Sky and discover that the apothecary is the demon Beelzebub who cast the plague upon Urbeth to take money from the populace. The party defeats Beelzebub and restores the city, lifting the plague.
Upon victory, the Crystal calls the four youths to praise them for their deed, and grants them the Alchemist crown.
Spoilers end here.