Luck. Pure, simple, luck.

Have you tried teleporters? You kinda have to look for Mantids or the Rock people, but it's damn satisfying to destroy the flagship's missiles from within. Dunno if you noticed, but all it's weapon systems are unconnected rooms, so no one is there to help the operator or repair it when you're done. You can whittle away the weapons and plink it down after that laughing maniacally.

Yeah, I did that approche before, but I always got fucked over with either boarding drones or having my pilot killed. It damn complicated and I've been playing with that same loadout for hours!

In the later phases, save your cloak for right when it's starting to do the missile swarm. Too early, and it pauses the charge. Too late and you get hit. I don't remember how the exact timing goes, though.

Beyond that, definitely wreck the weapon rooms. Don't kill all the crew, though, because that'll just make it kick on an AI to control the ship instead.

It's kinda been a while since I played, let alone was able to do well at it... I lost my save a while back, and just haven't picked it up again much. ~_~

With the advance edition it really gets hard because they send out boarding drones, hacking drones and mind control your crew members. If ANYTHING happens to your pilot. Even if he has to repair the cockpit it greatly increase yhe chance of loosing.

I do understand what you mean, the first thing yhat has to go is that damn triple missle canon (which teleporting is great for). The stealth Cruiser only has 3 weapon slots, you HAVE to get 2 other upgrades for your ship (Telepoters works best in this case.) The current weapons that comes with the ship are good... but without a Flak 1 and other room upgrades you can't get pass through the shield. And basically become a sitting duck. This game is so hard even with the right crew and equipment it also has RNG in play. I don't repair my ship, if at the last atand I don't get my repair becons before they are captured I'm screwed! You gotta save up that scrap for upgrades!

All and all, this game is really hard. But gosh darn rewarding one you beat that stupid Flagship.