The storyline of Omega takes place in the future era, 25 years after the Holy Wars of the 20th century. The goddess Athena is still on Earth after reincarnating to cleanse it of the agent of evil as she has done during millennia, accompanied by her Saints, fulfilling her duty of protecting peace on Earth, after her victories over antagonistic deities. Athena and a new generation of Saints prepare to face a new menace that lurks in this new era.