Shortly after the establishment of the Dominion elements of the fleet traveled to Char due to Sarah Kerrigan's psionic emanations. The fleet was led by General Edmund Duke and contained elements of Alpha Squadron. It engaged zerg and protoss forces in orbit but was defeated. Many ships were either overrun by the zerg or destroyed by the Protoss Expeditionary Fleet that arrived shortly after. With the ground forces suffering disaster as well the fleet fell back from Char, and later another fleet was defeated by the protoss.
In the years following the Brood War, credits that might have been better spent on expanding the fleet were instead spent by Mengsk in his hunt for Jim Raynor. Even so, by the time the Second Great War broke out, the Dominion had been able to construct several large fleets with advanced technology.
Crown Prince Valerian Mengsk took half the fleet to Char, where it engaged the zerg. The battlegroup suffered heavy losses, but with the aid of Raynor's Raiders and a xel'naga artifact the attack succeeded and Kerrigan was made human again.
After the battle, Emperor Mengsk demanded custody of Kerrigan; as leverage the emperor travelled to Char aboard the new flagship, White Star, at the head of the Dominion's remaining battlecruisers. The prince refused. The prince's now-renegade battlegroup and Raynor's Raiders fled and were pursued by the Dominion fleet. The renegades suffered near total losses, but managed to escape with Kerrigan to the Umojan Protectorate.
The fleet attacked the Hyperion above Phaethon. They continued firing even when Captain Matt Horner told them that Valerian was aboard, as Mengsk was willing to sacrifice anything to kill Kerrigan.
By the Battle of Char, the Dominion Fleet had around 50 battlecruisers. 25 were taken by Valerian Mengsk to Char, where 11 were lost in the battle that followed. A later confrontation with Arcturus Mengsk left all the remaining ships except Valerian's flaghip, the Bucephalus, destroyed or crippled, as well as a number from the other side.
↑Edmund Duke: "Protoss Commander, this is General Edmund Duke of the Terran Dominion Armada. You are in violation of our air-space and have endangered human lives in your reckless attack against the Zerg. I order you to withdraw your ships immediately. If you fail to comply, I will not hesitate to open fire upon your vessels." Tassadar: "General Duke, I am Tassadar, and you are well known to me. Whatever leniency I extended to you and your comrades before, may have been in error. If you persist in halting our course, we will burn your pathetic fleet down to the last man." Duke: "I'm going to have to assume that was a hostile response..." StarCraft. Vivendi Games. Level/area: Choosing Sides (in English). 1998.
↑Mengsk: "Congratulations, Kerrigan. You've beaten me again. Just remember that I'll be out there... waiting for you to slip up. Because sooner or later you'll make a mistake. And when you do..." StarCraft: Brood War. Vivendi Games. Level/area: Omega (in English). 1998.