How do you beat the Rebel Flagship?

[Maestro Ugo]

Thanks for the replies.

So in short, bombs / missiles are an absolute necessity in this fight, due to the shields. I'll try fighting the Rebel Flagship using less powerful ships again later (just beat it on Normal with the Crystal Cruiser type B; a boarding party composed of 3 Crystals and 1 Mantis slices things up real fast)

Most definitely not. A good ion weapon plus some fast lasers can be just as deadly.

[ApSciMorgs]

I kitted out my Kestrel Type B (called FSV Apollo) with a Soul Shot (does normal and ion damage; from Weaponanza mod), a Bust Laser Mk II, keeping the other two Basic Lasers, and maxed out my cloaking system. I also had the fortune of getting Stealth Weapons and Automatic Re-Loader. Only took two points of hull damage, and took out the Rebel Flagship in about a minute or two.

Sure, I used mods, and I was on Easy, but still, I think that was pretty good.