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 will rise after you board the newly flight-enabled Epoch, but only after you speak with Magus on a cliff; the outcome of beating him or him joining your party which does not matter.
As the Black Omen can only be reached by the flight-enabled Epoch. It can be entered in 12000 B.C., 600 A.D., or 1000 A.D. eras. should the party try to enter it in 2300 A.D., they will find the doors completely locked shut.
as the Black Omen can be fought a total of three times: during Antiquity, Middle Ages, Present. As mentioned, it cannot be fought in the year 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.
please 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.
Because the Black Omen is tied with the fabrication of time, several events that happen in the final dungeon, with the exception of the final battle on top of the Black Omen, will only happen once. Collecting treasures happen once only. Boss spots, Panels, and Ghaj are limited to just one battle, so having Ayla be present to Charm very rare items like the capsules is highly recommended in those battles. The Laser Guard defeated in the year 2300 AD at the outside entrance also counts. The only tie that is not linked is the final battle with Queen Zeal, where you can charm up to six of the rare and powerful Prism items (three Prism Helm and three Dresses).
Once you defeat Queen Zeal, she will summon Lavos to destroy and making the Black Omen vanishes before she disappears. The act will transport the party to the year 1999 and immediately to Lavos. If you went to 1999 A.D and defeated Lavos beforehand, you do not need to go through the sequence of battling Lavos again.