The Black Omen is depicted as raising after the Ocean Palace Incident transpires, led by Queen Zeal and Lavos. It subsequently exists in all the eras unless it is defeated in the past. The question is, why didn't the Black Omen rise originally? What changed when Crono went to the Ocean Palace that made it subsequently rise?
The answer lies with Schala. When Crono's group came around, she had only enough power to transport his two friends and Magus to safety. However, originally, she would have had sufficient power to remove herself, Queen Zeal, and another person (perhaps Dalton). Since Queen Zeal is suggested as the necessary key to raising the Black Omen, as she stays behind in the incident and communes with Lavos, her absence from the ordeal would probably nix the Black Omen's creation and appearance. This also provides for the pendant's history as a Kingdom of Guardia heirloom; if Schala had perished in the Ocean Palace, it would have been buried under the sea. However, if she warped out with a couple others, the Pendant would be safe on land to be passed down successive generations.
From: Common Questions