I've got to the mothership like 10 times but I can't manage to kill it. In my best attempt I got to the 3rd phase. As I like to use the engi ship, can u guys tell me of a engi ship build that works? I normally go with 3 attack drones and if possible 2 ion weapons( The only time I got to third phase I had 2 Ion weapons, 1 laser drone, 1 attack drone, 1 lvl 2 attack drone, lvl 3 cloak, blast doors, 2 shields and a maxed reactor).

A defense drone helps immensely because it shoots one of the three missiles fired and especially the boarding drones sent by the second form. Cloak is useful to dodge the laser volleys of the last form. If you don't have that, or it happens to be recharging, you'd better have at least 3 shields and decent engines.

Minimal boarding ability is also useful since the four main weapons on the boss are in isolated compartments and can't be repaired once the guy in the compartment is killed.

I have similar problem. Now I got to flagship with no problem, but can't win, usually because my weapons (at least i think its becasuse of that). Could you please tell me which weapons should i choose? I usually have cloack and boarding party, usually drone system (for defence mark I or II), but have no good ideas about weapons. I know, that killing all crew but leave one alone is important, but it's really hard for me. I fought with 3rd incarnation once, usually died at second part of the fight. My favourite ship is Red-Tail.

You made sure to turn your cloaking device down to power level 1, right ? In order to keep your cloaking-recharge cycles short enough to have it available for each "power surge"...

If you do that, you can generally earn enough time to defeat the flagship a 2nd and 3rd time the same way you did the 1st.

I always had it on three, I'll try that next time.

2 Shields? I don't think I have EVER been at the last Stand with less than full shields. With 4 shields its a cakewalk, only the rocket launcher can harm you.

Yeah, it helps immensely to have full sheilds. You can keep cloaking at 3, but you want to make sure you picked up the "cloaked weapons" augment along the way, so firing things like missles won't disrupt your cloak. While lots of drones is usefull for weaker enemies, I don't find them as good against the mothership. I did have a lot of sucess with a boarding drone (or two) keeping the Flagships personel busy while I transported rockmen (rockmen are the best for boarding with 150 hp, and fire resistance) over to attack their systems. Also, if you are fortunate enough to add a Zoltan or two to your crew, this frees up a power bar or two from your reactor for other good things like an additional weapon, or drone. Take as much time as possible earlier in the game ,to gain as much scrap, crewmen, augments, ect. Do your very best to visit as many beacons as possible to build your ship to the strongest possible before the "Last Stand". edit: btw, the "healing" drone can add quite a few points back to your hull during + *after* a battle with one of the first two incarnations of the flagship. This can be very usefull if you have plenty of drone parts, and there are no longer any repair stations to visit (and there seldom is, lol) You can even equip it right after a battle, heal your hull, un-equip it, and install whatever drone(s) you plan to use in the next battle

I beat it guys, all your tips where very helpful, ty.

Congrats! You are now an official Federation Cruiser Captain ;-)