Collective Hindsight, Book 1 — Aaron Rosenberg

STARFLEET CORPS OF ENGINEERS
The da Vinci comes across a strange runaway vessel that is giving off tremendous amounts of dangerous energy. However, the ship is not as strange as they think, as they've encountered it once before...

During the Dominion War, the U.S.S. da Vinci encountered this same vessel, and had to destroy it before it presented a danger to an entire star system -- not to mention to the war effort. However, doing so proved a challenge for the ship's first officer and second officer at the time: Commander Salek and Lt. Commander Duffy.

Now, over a year later, their successors, Commander Gomez and Lt. Commander Tev, must find a way to destroy a ship that is apparently unstoppable...