How?

[blazenwhiper]

So I finally got to the final boss (for the 10th time) with a boarding mantis party. first thing i did, take out their engines, then medical bay. then the weapons started going down.
Then the boss Jumps out of the battle.... What!? how do you jump to another sector with destroyed engines!? instantly lost 3 mantis, only had 2 engi's, 2 zoltans and a human.
So there was nothing to do after being cheated like that.

[5thHorseman]

They have special engines. They keep them in the same room as their extra drones (which you'll see soon) and superlaser (which you'll see eventually).

If you had mantises on the ship when you destroyed it, you'd have lost them anyway!

It feels cheaty and impossible to beat now, but if you keep playing there will come a day when you laugh at the Flagship.

[UltraMantis]

The Flagship is a very special creature. Regular tactics aren't enought to beat it, you'll need to counter some special tricks it has.

Instead of boarding the ship itself, it's usually the weapon bays that get 1st priority because they deliver most of the awesome damage and enemy crew can't defend well there.

Good luck! You'll beat it soon.

[NewAgeOfPower]

They have special engines. They keep them in the same room as their extra drones (which you'll see soon) and superlaser (which you'll see eventually).