This is Tully's* Flagship.
*sorta Tully's
Essentially the story here is that in one of the universes, Tully himself actually managed to conquer the flagship by disabling its advanced AI and commandeering the ship itself after the loss of his personal cruiser. Due to the severe damage and risk of friendly fire, Tully had to jump ASAP and repaired only the essentials, the primary systems, to a workable level. He also outfitted the ship with a much more potent laser artillery to help get the ship off the ground. The subsystems are nonfunctional and will have to be replaced, the rooms those subsystems were in need some new doors (that are already there, shhh don't worry about it), the reactor is in critical condition, and the ship is in desperate need of crew, but Tully himself is incredibly powerful and can manage for a while.
Oh, and random note: you'll have to rename Tully to "Tully" if you want the full experience, since you can't give starting crew different names. Whoops.
I released a small patch a bit ago to change the artillery up; laser artilleries will crash the game if shooting at a ship with more rooms than shots (since they shoot rooms exactly once), so I gave it a flak-style artillery with lasers to more or less simulate that without crashing (and increased the shot count slightly due to inaccuracy causing more misses). I also changed the missiles/drones count from 0/16 to 4/4 because, come on, both were very much used in the fight.
Download link here: https://drive.google.com/file/d/1gKnBmxRO3CTCUdm5DN3y_W2hF5aicab_/view?usp=sharing