The War of the Prophets, Millennium Book II by Judith & Garfield Reeves Stevens
The crew of the Starship Defiant is trapped in a future in which the Pah-wraiths have triumphed--as the greatest epic adventure in the saga of Deep Space 9 continues...
In the last days of the twenty-fourth century, caught in the crossfire of the apocalyptic confrontation between the Bajoran Prophets and the Pah-wraiths, Captain Benjamin Sisko and his crew face what might be the final millennium. On one side, the Pah-wraiths' new Emissary--Kai Weyoun--promises his followers that when Bajor's two Celestial Temples are restored as one, all beings in the universe will ascend to a new and glorious existence with the True Prophets. On the other side, the scientists of Starfleet predict that when the two Bajoran wormholes merge, they will create a Warp 10 shockwave of infinite destructive power.
With the Federation on the brink of collapse, and Starfleet consumed by Admiral Jean-Luc Picard's obsessive quest to build the largest starship ever conceived, Sisko enters the ultimate race against time for the biggest stakes of all--the survival of the universe itself.