Yeah, somehow I was able to grab that thing of beauty on my third playthough... My only problem is... I sometimes forget to look at the enemy hull level and my weapons would kill the enemy with my two Mantis commandos onboard.
Ah, I was using the Mk I. The only Mk II I have is for the Engi Cruiser, or "Drone Ship".
Still, fire bombs on the Rebel Flagship is just awesome. Easily nails the four weapons. Problem is getting the O2 offline, THAT is essential to me to stop all repairs and board/sap the ships systems.
Do you mind if I drop a few spoilers in order to discuss some tactics?
Well spoilerth. Eff it.
Do not kill everyone on board. That is all.
Fire bombs are nice. I like breacher bombs myself. They're pretty essential for getting around that ship's insanely high dodge and shields. I virtually always settle in on nuking the missile command first, followed by the ion cannon. After that she's pretty well neutered.
Then it's on to the engines to remove the dodge and everything else generally follows.