Six years before the events at the focus of the series, one hundred orphans from Japan are sent to different parts of the world to become legendary warriors known as "Saints", who are the soldiers under the command of Greek goddess Athena. These warriors are under the protection of a celestial constellation.
The power of the Saints originates from the understanding of the nature of the "Cosmo", an inner spiritual essence, originated in the Big Bang. The concept of the "Cosmo" advocates that each atom within a human body resembles a small solar system, and since the human body consists of billions of atoms, the totality forms a "small Cosmo" or a "small Universe". Each person's Cosmo has its own unique signature. The Saints take the knowledge of the Cosmo to the next level: since humans are composed of atoms, humans should be able to use the mysterious forces behind the atoms to achieve super human feats.
The story focuses on one of these orphans named Seiya. He is sent to the Sanctuary in Greece to become the Pegasus Saint. After six years, Seiya becomes the Pegasus Saint and returns to Japan to find his older sister. Because his sister disappeared the same day Seiya went to the Sanctuary, Saori Kido, the granddaughter of the person who sent all the orphans to train, makes a deal with him to go to fight in a tournament called the Galaxian Wars, where the orphans who survived and became Bronze Saints must fight to win the most powerful Cloth: The Sagittarius Gold Cloth. If Seiya goes to compete there and wins, Saori would start a search to find Seiya's sister.
During the series, Seiya becomes the partner and friend of other Bronze Saints: Shun, Shiryū, Ikki, and Hyōga. As the myth of the Saints, they must fight together to protect the reincarnation of the goddess Athena from any danger, as their predecessors have during millennia.