The Black Omen (黒の夢 "Kuro no Yume"?, lit."Black Dream") was once the Ocean Palace that was destroyed by Lavos. In the alternate timeline, it was later transformed into a flying temple infused with the near-infinite power of Lavos by using the Mammon Machine. The Black Omen serves as the final dungeon in the game — although entering it is actually optional, as the player can choose to fight with Lavos without entering the Black Omen — where the party has to go through and defeat the evil Queen Zeal and face Lavos in all its forms.
With the immortality bestowed upon her Majesty by the Mammon Machine and its connection to the Time Gates, Queen Zeal is prepared to wait out the millennia until Lavos awakens and rains its havoc upon the world. Until the party enters this vast dungeon and defeats Queen Zeal, it will appear at all points in time (save for Prehistory). People will actually not pay it any mind, since it has been floating in the sky for thousands of years, except for an Imp worshipping it in Medina's park.
The player may escape through the Time Gate inside Lavos after Lavos' shell is confronted by the Black Omen. This will cause Gaspar to have a new dialogue (after his mentions of the game's side-quests):
This line can be attributed to a rushed translation; it does not exist in the Japanese version. The more accurate DS version's scripting replaces this line with:
The Black Omen can only be reached by the flight-enabled Epoch. After it rises from the ocean, it can be entered in 12000 B.C., 600 A.D., or 1000 A.D.. Should the party try to enter it in 2300 A.D., they will find the doors locked shut.
The Black Omen can be fought a total of three times: during Antiquity, Middle Ages, Present. As mentioned, it cannot be fought in 2300 A.D. (except using an Action Replay cheat in the DS version as described earlier), as the entrance will be closed. Also, it did not exist in 65,000,000 B.C., since it appeared later, in 12,000 BC.
Note that if the player wants to beat it multiple times, they must do it back through time (i.e.: Present, then Middle Ages, then Antiquity). Destroying it at an earlier time will erase the existence of the Omen from any future time periods.