I was doing great with a fully upgraded ship with cloaking, crew teleporter and 3 burst laser IIs.
I did great on the 1st and 2nd stages, using the teleporter strategy and teleporting inside his weapons. At the end of the 2nd stage, there was a repair station nearby but that has happened to me before. (http://www.ftlgame.com/forum/viewtopic.php?f=8&t=14211)
I just went on. The boss definately had the upper hand. By the end, about half my rooms had breaches, allowing me to get absolutely no where to fix my systems, and a few of my rooms had fires. On top of that, my hull was dangerously low. At that point, my heart beat was over the roof. I had totally ditched the teleporting strategy, making me take lots of hits. Although miraculously, my weapons were unharmed
. I just randomly aimed my lasers and turned on autofire, and hope I won. I ended up firing a barrage and none of the lasers missed ( 
) destroying the flagship while I had 4 hull left. All my crewmembers survived, and I was half dead from intensity by then. So theres my story. Hope you enjoyed. 
