Once you defeat Queen Zeal and she summons Lavos' power, you see a scene where the Black Omen appears to be hovering, not above land like in every era it appears in, but over Lavos in 12,000 BC. After this scene you begin the fight with Lavos' Shell. Now upon trivial evaluation the extent of the continuity and plot issues posed by this event has eluded me, and I still can't intuit the solutions, but I feel like throwing out a few ideas and seeing what the community comes up with will be an effective way to plausibly explain what happened.
A few important issues to address.
The Omen is no longer in its original time and position.
Even if you start in Antiquity, the Black Omen has at least moved to be positioned over Lavos. I posit not that the Omen is Epoch-esque, that is to say being capable of time travel or much physical transport, but that due to the Mammon Machine's heavy integration into the structure it is inherently linked to Lavos. Perhaps when the controller (Lavos Conduit?) of the vessel, Queen Zeal, formally made a plea to Lavos the vessel responded and was warped to the beast. This is evidenced by no real scene of transport, it's almost as if the machine immediately arrived above Lavos.
Losing to Lavos results in the same scene in 1999 A.D.
Now this is almost certainly a development oversight. It's conversely unlikely we're meant to read too far into this, but that's what we rabid fans do eh? When I try to reconcile this plot wise, it is still very strange. It seems unlikely that Lavos would be able to emerge, kill our brave heroes, and then quitely rebury itself to emerge again in 1999. Ignoring the option of writing it off as a dev. issue, I can't seem to reconcile this.
Beating the Lavos Shell after running through the Omen eliminates the Omen from the time of entry.
This one requires a bit of explanation. What this means is, if you enter the Omen in, say, 1000 A.D, beat the Lavos Shell, then take the gate back to the end of time, the Omen is gone from 1000 A.D. However, there is still only one Omen in 12,000 B.C. and running through in 600 A.D. and 12,000 B.C. have the same cut scene with Queen Zeal. Once again it's easy to write this off as an oversight, and it likely is, but I'm sure there's a canonical way to decipher this.
