The storyline of Omega takes place 25 years after the Holy Wars of the 20th century narrated in the original manga and its anime adaptation. The goddess Athena is still on Earth after reincarnating to continue her duty of protecting peace against several antagonistic deities. Athena and a new generation of Saints prepare to face new threats that lurks in this new era, in which Pegasus Seiya, the protagonist of Kurumada's manga, is revered as a Saint of legend and one of Athena's Gold Saints.
The first part of the series is the "Mars Saga" (マルス編 Marusu Hen?), introducing the new Pegasus Saint Koga and his friends Dragon Ryuhou, Lionet Souma, Wolf Haruto, Aquila Yuna, Orion Eden, and Aria and the beginning of their fight against the God of War Mars in his quest to capture Aria to become the new Athena. The second part is the "Zodiac Temples Saga" (十二宮編 Jūnikyū Hen?), featuring Koga and his friends fight against the many Gold Saints who have aligned themselves with Mars in their fight to save Athena before it is too late.