I could see a Co-op mode where the two players are simultaneously playing their own independent game with their own timelines in parallel universes.
When one player enters a battle, the other player gets the invitation to join it. And periodically (maybe once each player has simulated at least a year since the last event), a "dimensional portal" would open up and allow the players to choose among various options for sending aid between the two universes.
Aid options might be like:
-Since the Skylaxians like player A, they can increase the attitude of the Skylaxians towards player B by X
-The Andors are under attack in universe B, have the Andors in universe A send a few armadas through the portal to help.
-etc
just an idea...