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I did the run with the `red-tail`
It was to a run with luck of shopping, the RNG decieded that I can get nothing useful after sector 4 from store. But I am prepared for that so I grabbed a chained-ion in sector 3 and a weapon automated realoader in sector 2. I did hesitate for a while but it proved these are the keys that grant me the power to kill most of the ship. The final weapon-set I got when meating the flagship is chain-ion plus three basic laser. Not my usually style but it can do something - such as make the rebel fear basic lasers
The really problem is that I did not get the cloak. I was mis-calculating the scrap income at the first so missed a cloak in early sectors and never seen it again. I met the teleporter near the end of the sector 7, and I consider it not worth it (I did not have the 4th layer of shield at that time and I heard the flagship are connected as hard mode). I am not a big fan of hacking or mind control (seriously, is the mind control over-powerless?). The only extra-system is the drone control. While many others citing that the drones block the missle with face and that sucks, my drone once shot a missle and blocked another with it face, which made me laugh for a while.
The fight with the flagship is extremely hard but the RNG considered that I shall be granted the true power of miss so I sit and see 12(or more) incoming fires either shot by the defence drone or flying aside from my ship. For a while my shield-man look bored. But it was indeed difficult. As I have said the weapon set is heavily based on the chain-ion, which is an ion weapon, which sucks when the target cloaks frequently. The first stage takes like 15 minutes or so and 75% of my hull. Luckily there was a repair station sitting near the base. During the second stage, due to incapable to de-active the main weapons of the flagship, the power surge is a pain, much more painful than I have imagined - I though it would be like the Fed-A back before AE but I was far wrong. I managed to maintain 10 hp at the end of the stage 2. The stage 3 is much easier. It pours its crew into my ship but I do not care for I have door level 3 plus 2 mantis. The chain-ion kills the super shiled easily and than the normal shield. The power surge never got sychronized with the volley so not really a problem. My crew died a few, but the flagship was boomed; Yet I got 3 hp left.
One tip: The Def-Drone-Mk-2 can shoot the ion but if you fire a laser and the ion together, it will shoot the laser and miss the ion. In that way I handled some heavily-droned ships. Thanks god that the flagship stage 2 does not have one.