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Mind controlled Zoltan firing at my weapon systems, massive boarding. That was pretty much it. Mind control and no repair when you wait on your base broke my back.

I was having a AWESOME run with one of my own ship mods (In AE) until I fought the flagship. I got the zoltan ship unlock event in sector 6, which gave me a zoltan shield. I also had a experienced mantis boarding crew and a veteran weapons guy. When I got to the Last Stand, I worked through all of the Elite Fighters without much damage to then face the 1st stage of the flagship. I teleported in to the missile room and disabled it. While this was happening the flagship launched a hacking drone on my O2 system. I had a excellent defense (due to my super shield absorbing the first few missile volleys, and my level 4 shields taking the rest.) and the battle was going good for me, then the flagship started hacking the O2. Being the Rebel Flagship, it had a top level hacking system, which depleted my O2 faster then it could replenish it, suffocating my entire crew and prematurely ending what could have been a victorious run. Long story short, I got the Slug Interceptor treatment.