Well... it could be that Papalymo will use Tupsimati to cast "White Dalamud" to imprison the new primal, but given he didn't have the time to prepare it won't last indefinitely and as we saw with Bahamut it's kind of a flawed move. Granted said primal will likely be less powerful than Bahamut so it'll be imprisoned longer, but we'll still be aware it won't last forever and we need another, more permanent answer. Enter Omega.

Explains the explosion (primal breaks free) and why we're still going after Omega. Also provides a handy cutoff for 3.5 before 3.5.5.

With what we have now, this is my best guess. I can't approximate the actions and purpose of every character, but...