Another FTL Run.
This time with the Zoltan A. Didn't think I was going to make it until I realized I had this:
I had, by the end, 3 mantis, 4 zoltan, an engi, a hacking drone, a cloning bay, and the augment that let me warp through the zoltan shield.
Then the flagship came. And I was ready.
Then my strategy cam full force. Send in the mantis. Take out the missile launcher. Then take out the laser beam, and ion cannon. I was then basically impervious. I left the guy in the laser cannon alive, because the amount of crew carries over from multiple stages, and if you kill all the crew, the aggressive AI takes over and repairs everything.
Then, hack a room, and send in your people to that room. Because of the fact that the people have to break doors to get in, the hacked room gets destroyed, then the crew runs in to try and kill my mantises. They die from that attempt, because the door locks behind them, and they have to break out, and by the time they get close, my crew has already killed them.
This is me destroying most of the flagship once I killed the crew.
Next level was easy, did not take pictures.
Finally:
