There once existed a land where man and gods coexisted peacefully. This place was known as Angel Land. This land was ruled by two beautiful goddesses: Palutena, the Goddess of Light and Medusa, the Goddess of Darkness. While Palutena loved the mortals and helped them cultivate their crops, Medusa despised them. In her hatred for them, she destroyed the crops that the mortals toiled to grow, and turned humans into stone. Enraged, Palutena turned Medusa into a hideous monster and banished her into the Underworld.
Medusa would not go quietly, however. She began building an army of demons and monsters. With this army, she broke out of the Underworld and waged war against Palutena's army. The latter's army suffered many casualties and Palutena herself was imprisoned in the Palace in the Sky.
Meanwhile, a young angel named Pit was trapped in the Underworld. Using the last of her power, Palutena granted Pit a magical bow and entrusted him with the duty of defeating Medusa and saving Angel Land. To do this, however, Pit would have to reclaim the Three Sacred Treasures. These sacred items rightfully belonged to Palutena, but Medusa stole them and gave them to her three most powerful minions. Pit would have to escape the Underworld, which would prove easy since most of Medusa's forces were in the Palace in the Sky. But Pit would have to travel through the two other realms, the Overworld and the Skyworld before reaching the Palace in the Sky.