Damn shame buddy....
Next time, if you dont get any damaging weapons, you can kill all the crew, let the AI take over the ship and then destroy all systems the AI has repaired for an additional 1 damage to the hull per system This will require you to sacrifce a boarder for each boss stage - as the boarder will go down with the flag ship when it jumps/blows up.
Congrats on getting to the flagship !
Keep on FTLing
