The interior of the Starlight Megalodon became baptized in war and paralysis. Behind the scenes, the captain's faction and the admiral's faction waged a frigid war on the ship's internal network and all of her automated systems.
Meanwhile, in realspace, Flagrant Swordmaidens and the Vesians fought over the vault which they believed stored a batch of high-grade life prolonging serum and other valuables.
These two interconnected battles threw the entire ship into disarray and prevented her from engaging her most potent defenses to annihilate the humans or the AIs that took up arms.
The chaos wracking the ship lessened almost every human and AI's attention away from the neutral Research Department. The evenly-sided stalemate also ensured that the conflict wouldn't be resolved within a short amount of time.