Oh man.
I nearly had a Fuck Me! moment... i was playing a modship, and after a rough rough start got into a nice groove of pillaging and kicking FTLs ass (for a change). I was ready for the bossfight at the end of sector 6 and pretty much just beelined for him from there.
So i herp-a-derped my way, picking up some final upgrades, lvl3 Doors, an extra level for drones and weapons just to be safe, and just FLATTENED the flagship in stages 1 and 2. Stage 3 was hillarious though. Clearly i had just stopped paying attention because i made a proper mess of EVERYTHING.
The hull smashed to bits, life support and medbay breached and destroyed, and ... then i left the ship doors open. And tried to vent a fire. With ship doors open.

No medbay, no air, and 2 crew already on minimal health. Well, if you thought i repaired life support first, congratulations! You're NOT and idiot. I am, and i repaired the medbay before realising what i did wrong.
I must re-iterate that i FLATTENED the flagship in stage 2, which is rightly regarded as the killer stage... the notion of actually losing this run was forgotten long long ago, way back in sectors 4 or 5, and yet i managed to (nearly) snatch defeat from the jaws of victory with such appaling stupidity like you've never seen.
So 2 crew dead, one nearly there, one Rockman still trying to wreck the triple missile launcher, and i'm shitting myself now. AND the Super-Duper Mega-Shield pops back up.

I scrambled the Rockman back onboard and tried to restore life support but no dice. There was no air to breathe and the last human died. What a mess...
At this point it was a race between one lonely Rockman barely surviving in an airless medbay, and the badly damaged Flagship with the triple Heavy Laser, triple Missile Launcher and one more surge multishot. If you're gonna be dumb you better be lucky. I was, the cloak still hadn't burned down completely and no enemy shots hit the weapons bay.
The flagship was sliced by a Pike Beam, my ship had 3 hp left and one Rockman will have a hell of a story to tell his grandchildren. And I have a victory to be proud of. The dumbest and least-deserved win ever. By far.
By far...