Starship Theseus (The Hive Invasion Book 3);

Interstellar war is just the beginning
Richard Hammett is no longer a captain in his beloved Spacecom. He's an admiral in the brand-new Colonial Forces in the Naxos system, tasked with defending the colony from the aliens of the Hive – and from the vengeful ships of Spacecom as well.
When a scouting mission in deep space reveals the location of an alien Gate, Hammett finds himself surrounded and trapped. A Spacecom fleet blunders in, looking for Hammett to place him under arrest. With the aliens closing in, the two human fleets set aside their differences to battle a common enemy.
A desperate gambit leads to a once-in-a-lifetime opportunity to strike at the heart of the alien empire – but if the aliens are defeated, Hammett's new allies will turn their attention to him. They see Hammett as a traitor and a mutineer, and if they can get their hands on him, he'll hang.