In a time where man and gods coexisted in harmony, the kingdom of Angel Land was ruled by two goddesses: Palutena, the Goddess of Light, and Medusa, the Goddess of Darkness. While Palutena administered the light and helped the mortals cultivate their crops, Medusa despised the mortals and used the darkness to destroy their crops and turn the mortals into stone. Enraged, Palutena transformed Medusa into a hideous monster and banished her into the dark underworld.
But Medusa would not go quietly. She assembled an army of monsters and evil spirits of the underworld to conquer Palutena's home, the Palace in the Sky. War erupted and Medusa's minions overwhelmed Palutena's army, eventually imprisoning the Goddess of Light. Medusa then seized the Three Sacred Treasures, the Mirror Shield, the Arrow of Light and the Wings of Pegasus, and gave them to her most powerful minions.
Defeated and imprisoned, Palutena's only hope was to seek the help of Pit, a young angel trapped in the Underworld. Using the last of her strength, she sent Pit a magical bow. Thus, Pit set out on a quest to escape the Underworld, retrieve the Sacred Treasures that would help him defeat Medusa, rescue Palutena and restore peace to Angel Land.
Pit retrieves these three treasures and battles Medusa. Having won, Pit travels back to Angel Land, where the newly restored Palutena thanks him. However, if the secret ending is reached (all upgrades and hearts), Pit will be turned into a teenager and will receive a kiss of gratitude from Palutena.