You know those runs where you fall behind and repeatedly get beat up? I just won one of those. I was in the stealth ship, with three female crew members who each had a "pet" Engi (the three female crew was on purpose, the engi thing just happened). We got shields a little late and were low on fuel and health when we did, and never really recovered; past the 3rd sector, we never went above 10 fuel. Our systems a decent shape, we focused on gaining weapons, but we never found any good ones. The only weapon shop we ever found sold a hull laser and an heavy ion; I bought the heavy ion despite it being basically the worst weapon in the entire game, I was that desperate.
Near the 6th system exit, we were ambushed by a heavily armed rebel ship. Both ships pounded each other in a brutal fight, until we found ourselves without cloak and the enemy charging a halberd beam. We couldn't do enough damage to kill them and dodging was out of the question. We fired a last volley in defiance... and they surrendered, giving us a small bomb. Then while repairs were underway on our ship, their's exploded from fires in the shield room.
At that point we were doing... ok, but we had nothing but the starting weapons and a small bomb. The plan was to keep upgrading the defensive systems while holding some scrap on hand to get better weapons at a shop that sold some. We found a shop in the seventh sector, right before the exit. They had no weapons for sale. Resigned, we blew our weapons fund on a drone bay and a single mk 1 anti ship drone.
The Chick Flick entered the Last Stand with a mini-beam, a double laser, a small bomb launcher, and a mk 1 attack drone. We had no crew teleporter; the above was the complete extent of our offensive abilities. The scrap from one last blasted rebel ship let us upgrade to a third shield layer, and then we were off to face the giant rebel flagship with with our dinky weapons. The fight was surprisingly uneventful for the first two engagements; we routed all power to defensive systems until their shields suffered two bomb hits, then used the double laser to keep the shields down and switched on our other weapons systems to carve them up.
Then, we got to the final fight. The pilot and gunner needed to stay on their posts, so the crew we used to repel boarders was mostly engis, and on top of that we had to reserve our cloak for the superweapon and take missile hits. An early hit to the door systems went ignored while the crew cycled between the medbay and repelling boarders. This came back to bite us when the entire center of the ship caught fire. We brought the door systems online and took out their missiles, but not before Charlie the Engi was taken out when the massive brawl in the engine room got hit by a missile. The Chick Flick was heavily damaged, on fire, and Natalie lost her Engi friend, but by god we were victorious when we should have been dust six sectors ago.