So I've finally beaten the game, using the alternative layout Kestrel cruiser. My loadout was: Maxed out shields, engines, O2, medbay and doors (naturally) Weapons pre-igniter, shield charge booster, engi med-bot dispersal (this was huge) Maxed out cloak (used to avoid drone surges and the 'super-weapon' of the final boss) Phase one and three: Burst Laser Mk. III, Glaive Beam Phase two: Burst Laser Mk. III, Small Bomb, Ion Blast Mk. II The fact that I went with 'unconventional' weapons for phase two saved my rear end. I also had a drone control with two Defense Drone Mk. II, but I never used them. I think the deciding factor was that I tried out new weapons and that I had gotten a lot better at micro-managing my crew. The fact that my repair team consisted of two Engis both named 'Jones' probably helped too. I was amazed how much the med-bot augment helped me out with emergency repairs during low damage moments in the final boss fight. I could cut power from my engines and pump my medbay and O2 up to full and go into breached rooms without worry, then have my engines back to full before the next enemy push. What really helped me out in the early game was picking up two scrap recovery arms early, and not giving up the last one until sector seven. Because the ship starts out with four weapons you'll probably end up with a maxed out weapons skill on one of your crew members by the time you hit sector two. That was a big help as well, especially since the ship is already quite potent in the early stages anyway.