Uber Ships that get pummeled by the Flagship

[TheRealTeo]

We've all had that FTL run. You completely cruise through sectors 1 through 7, reducing any ship in your way to a heap of space debris quickly and devastatingly. Or perhaps your ship is equipped to outlast anything thrown at you. You feel invincible...

And then you fight the Flagship.

Your ship goes up in smoke within a minute and your ship promptly explodes.

So, what ships have you flown that feel absolutely ubercharged during the main game, and have your @$$ handed to you on a silver platter when you go to fight the flagship?

Most recently for me, I was playing Stealth C on easy (call me what you want, Stealth C is hard enough as it is) and by the time I made it to the Flagship, I had:
Level 4 Shields w/2 star crew
40% evasion from crew, pilot, and thrusters
TWO Defense II drones
TWO Flak II guns w/1 star crew
And level 2 hacking, to counter the Flagship's hacking

And for some reason, halfway through the fight, my drones decided to stop aiming at missiles. About every missile thrown at me landed. Things began to fall apart until I was ultimately killed. God f***ing d***it.

Anywho, let's hear your your stories.

[DudeNamedEvan]

Kestrel A, I had FULL EVASION WITH A MASTER PILOT, three shields a burst mk2 chain and charge lasers and when I got past 7, I was convinced I was in sector 6 , and when I got to the flagship, everything they had slammed into the pilot, killing him and setting us to 0 evade and then they proceeded to reduce the kestrel to space dust, kill every federation supporter and enslave the galaxy...