Came so, so close twice in a row. First time around, I had full cloak and shields, and a loadout of Pegasus, Ion Blast, Burst Laser I and Fire Bomb. With Stealth Weapons.
Pegasus and Fire Bomb worked beautifully to take out the forward weapons rooms, and cloaking allowed me to dodge the missiles, shield blocked everything else. Only took two damage in Phase 1.
Drones were annoying as hell in Phase 2, but cloak helped with that, and my bombs took out all the forward weapon systems while I teleported my two Mantises onboard to fuck some shit up.
Unfortunately, I wasn't paying attention and they killed off all the crew. Which meant it jumped out. With my Mantises onboard.
Phase 3 was going pretty well....and then I ran out of missiles. Ion and Burst Laser simply couldn't penetrate. And it wouldn't let me teleport anybody onboard to wreck the shield generator. Jumped away, hoping to find some more missiles but I couldn't and then I was out of turns.
Started over with a first run in a Zoltan cruiser. Skated through the first 4-5 sectors like a boss. Zoltan shields mean basically never taking damage the first couple of sectors. Accumulated a ridiculous amount of scrap, so that by the end-run, I had a Heavy Ion, a Halberd Beam, and two Breach Missiles. With nearly 60 missiles in inventory. And full cloak. Hells to the yeah.
Phase 1: Over so fast, it caught me by surprise. Racking up 8 hull damage every time I fired a pair of missiles, plus another damage when the subsystem was destroyed meant that it went down hard and fast. No damage taken, and still had 50+ missiles.
Phase 2: )(*#^(&$^#*&(&#&* DEFENSE DRONES. I needed bombs. Or a teleporter, although my crew was mostly Engis and Zoltans. And the drone swarm kept whittling down my shields as fast as I could recharge them. Plus MF'ing boarding drones (see "crew mostly Engi and Zoltan").