Fuck you, Rebel Flagship.

[Riddlewrong]

I'm pretty sure the only way to beat this thing in AE is if you get lucky enough to have the perfect well-rounded ship build when you arrive, and pray to almighty Zeus you don't get hacked in a critical system.

In my latest playthrough:

I somehow managed to beat the first two phases with Kestrel A using Burst Laser II, Flak I, and Halberd Beam I. These were the only weapons available the entire trip, and I had to sell my Artemis at a crucial point early in the game to afford repairs. My crew was very minimal -- there were no recruitables when I had the scrap (I got lucky and picked up a Mantis off a random event, though), and I made it to the final beacon with 4 crewmembers, way too much scrap, and nothing to buy. It always seems like it's the perfect storm of defeat when you reach the Flagship. I got to phase 3 of the Flagship battle with all of my crew alive (3 human, 1 mantis) and the enemy boarded + mind-controlled my only mantis crewmember. So fucked.

What's your Flagship horror story?

[JonasTheRoman]

Last time the Flagship hacked my weapons!
This is very annoying, especially since I used a Glaive Beam, so the first stage became veeeery long.

Luckily my boarders were able to take out the rocket launcher, so the flagship wasn't able to hurt me.

So in the end the hack was not horrible (like I thought at first) but only annoying.
The flagship cloaked and hacked alternating, but I was able to destroy the flagship eventually, by small-bombing the important systems and having luck with the periods of cloak and hack.

[r543]

AE Flagship is completely different than the normal one:

The first phase uses Hacking, which might or may not be a problem:

I've noticed that the enemy hacks always select the same system(or at least on easy), not sure if it changes every run or not, but it's very annoying on some ships.

Here are the ships and systems I noticed:

Hacking:

Zoltan A(or was it B) Cloak

This is very bad because you can't use your Cloak AND your Ship is split into 2 parts, so your crew can't get to the other part.

Zoltan C(Shields)
The Flagship hacks the shields here, shields,drones(if you have important ones) and weapon systems are the most annoying ones.

Federation B(O2)
Not too much of a problem, exept for running out of O2

Engi B(Doors)
I haven't tested this on the flagship, but on an other hacking ship. Doesn't allow you to move anywhere, but all systems still work.

Krestel B(Teleporters)
You might think that this one is the worst if you have 2 mantis to board the enemy weapons, but the Flagship fails at using it.
It always used the hacking when it cloaked, which didn't allow it to teleport my members back(you can do it, but the hacking can't, like in older ftl versions). Maybe this only works for easy.

Phase 2 hasn't changed that much, Boarding Drones are still annoying, but that's it.

Phase 3 is way more annoying now.
Back in old FTL, you almost won here, there wasn't too much to go wrong. Now it's a big problem. You get 2 boarders AND a mind controlled player. Don't forget that you can't board the rocket launcher and take it out at the beginning because of the zoltan shield.
On my Red Tail run(Krestel B, Hull Laser 2, Hull Beam(not powered) and Ion Blast 2(very good but if it misses, you don't have a chance), I got destroyed when the ship used the power surge attack.
My cloak had the cooldown on and my level 4 engines got hit, so I had around 20 evasion. Right before firing that power surge, it decided to control my pilot, so my evasion dropped down to 5%. All shots hit, my hull hp went down from like half to zero in less than 5 seconds, couldn't do anything against that.
So yeah, it feels like mind control is needed here, I probably should've got that instead of the drones which I didn't use.

[Nukeknockout]

That's not actually true - the flagship randomly selects a system to hack, same as every other hacking ship. I know because I've actually jumped away when my shields were hacked to come back to a drone latched onto another system and because I've occasionally shot down eight hacking drones in a row with Defense Drones only to see them try for different systems every launch

For phase three, a Defense II cuts down on the incoming lasers somewhat and sending a second crewman into the cockpit would at least increase your evade somewhat. It's easiest on phase three to counter their mind control with your own mind control, but its also very possible to bombard the system until it explodes or latch a hacking drone on it.

But as for my horror story - I was in the Simo-H, with a good game going on so far. Had a BL3, starting laser, and swarm missiles going up against the flagship. Also mind control, drone control, Zoltan shield, pre-igniter, just an absolutely brilliant run. Round 3: Mind control pilot, counter. BL3 missed five shots on its Zoltan shield, Swarm missed three shots on its Zoltan shield. Flagship fires three lasers, hits three times. Fires three missiles, defense drone kills one other two hit. My Zoltan shield down. Flagship power surges just before my drone can start fixing the Zoltan shield, hitting my drone bay...and starting two fires thus shutting off my Beam drone and shortly thereafter, my defense drone.

Ten more misses for my second volley, then the flagship fires missiles. One missile is spoiled on my supershield, the next two hit the drone bay. After a few rounds of mind control/counter and taking consistent damage thanks to repeated missile hits my drone bay is completely offline. Shortly thereafter, the Flagship overcame my ship completely.

I am irritated only because I really did have a chance that time.

[Reptile]

Before I wasn't scared of the first phase at all but now the hacking made it so much pain.
In one of the recent runs i had i had a completely insane build of few burst lasers and 2 pike beams or something like that with weapon pre-igniter. I sliced thru every enemy I met so I thought I had a good chance at beating the boss. Ok got to sector 8 jump to the boss and the motherf*cker knew, he fucking knew that I had the pre igniter. Now I knew he is gonna cloak so I wiated after his cloak runs out, but right before he cloaks he sent a hackig drone to my weapons. He was cloaked and I was just straing as my wep charges went down. Alright I can still beat him, I said to myself. But then even with 50% dodge he still hit every f*cking shot. He hits my engines, weapons shields, EVERYTHING. And I am completely f*cked at this point and all because of one hacking drone. I feel like the boss is so mcuh more random now. To the point where the only good tactic is to have cloak and swarm his shields with everything you have or I just really suck at this game (probably the second one).

A little OT: Did the chance of fire on all weapons got increased? Because I noticed that maybe half of hits I get result in fire even though the weapons have a low chance of fire. Was that changed in AE?

[Captain_obvious]

I learned the hard way last night that ion builds have a big chance of becoming completely useless against phase 1 if you get hacked in the weapons bay. Between the cloak and the power drain, you've got zero chance of building up enough charge to take down the shields.

[slattikarma]

I learned the hard way last night that ion builds have a big chance of becoming completely useless against phase 1 if you get hacked in the weapons bay. Between the cloak and the power drain, you've got zero chance of building up enough charge to take down the shields.

Yep, my early Engi A run led to doom because of this.

I think if you are planning on an ion build, you need to specifically plan for some kind of counter for hacking in Phase A of the flagship. The most effective is probably just to have hacking, so you can hack his hacking bay and neutralise it. Some kind of drone defence or a bomb/missile weapon to take out the hacking bay is probably the next best thing.

BTW, is the boss's hacking target random? It seems to always go for my strongest points. Probably coincidence, but whenever I've had strong weapons, it always hacks my weapons, other times when I was built for boarding, and couldn't give a stuff about my weapons, it hacked my engines and then shields.

[Terminus Paragon]

On my second to last playthrough, arguably one of my best runs, with the FNC "Supernova".

I got to Sector 5 or so. I had zerged through all previous sectors and had gotten two MK1 Flak Guns, a Breach Bomb MK2, and a Burst Laser 2. It was the perfect arsenal for me; a pick-and-choose of accuracy, precise destruction of critical systems, and sheer (innacurate) destructive power.

And then I ended up botching up two boarding runs, killing my two Rockmen and my Mantis. So I was left with a human and two Engi.

By the time I got to the Flagship, the Engi had both died, and I had gotten a human and a Mantis aboard my ship as replacements. I was desperate. I had run out of fuel in Sector 7 and nearly been annihiliated after a super-powerful pirate cruiser responded to my distress beacon. I lucked out by getting full repair and ressuply in S8, and full shields, and power for all my weapons, and Level 2 Artillery beam. I was really hopeful; I was pretty sure I couldn't beat the Flagship, but maybe I could defeat Stage 1?

So I confront the flagship.

And get PUMMELLED.

Within 4 minutes, the human I had just gotten was dead, my Mantis (which I had tried teleporting into one of the weapons) was trapped in the Teleporter room when it got hacked, and my first human, brave Captain Auridax, who had survived from the very start, was left to combat about a trillion fires.

Eventually, I just got confused by all the explosions and flashing lights and fires and just watched hopelessly as vital system after vital system turned red and as missiles cut devastatingly into my hull points.

Within 5 minutes of the battle starting, Captain Auridax was just scattered bits of scorched flesh floating around in vacuum.

I raged for around 2 minutes afterwards; the skill curve between normal ships and the Flagship is ridiculously steep.

Still, at least I got two great screenshots out of the whole ordeal.

[Captain_obvious]

Okay, just now I was on the verge of completing a great run with the Nisos. I had been absolutely decimating just about everything I came across with the combo of Ion II + Vulcan + Artillery beam. I had cloaking and hacking for utility purposes, not to mention Engi Med-Bots and Automated Reloader. Absolutely breezed through the first two sections (survived being hacked in the cockpit), so I figured the last one shouldn't be too tough.

Ho-boy.

Mind control hits my cockpit again, only this time turning my pilot into a super-Saiyan knocks out my evasion in seconds. Three missiles hit, leaving breaches and fires all over the ship, and knocking out the Arty beam. Enemies beam on as well. While I desperately try to teleport them home with the hacking drone, the mind controlled guy heads for the engine room and pummels down my Zoltan engineer before the mind control runs out. No engines, fires everywhere, next volley of missiles takes out weapons and oxygen, GG.

Yesterday I beat the game with the Shivan, and it now feels like the main reason I won was being lucky in what systems the hacking and mind control targeted each time. Kind of blows, TBH.

[slattikarma]

I've never had a massive problem with mind-control, it's normally just been a pain.

I let the mind-control guy start to destroy the system room he is in, then just as it's about to lose a bar, I rush another guy into the room to fight him (allowing the system to stay preserved)... then I let them fight it out for a bit until my non-mind control guy is about to die (because the mind-control guy is normally boosted by the mindcontrol) before rushing him to the medbay and replacing him with another team-member. Then this guy will continue fighting until the mindcontrol wears off (normally leaving the mindcontrolled guy with 50% health) then I rush both to the medbay, so everyone is at full health before the next mind-control starts. I can normally destroy the enemies mind control room before round 2 or 3.

It's worse if your pilot gets mind-controlled, but otherwise, i've never been defeated by it.

I also normally try to kill as many guys off in the flagship in phase 1 or 2 so that there won't be many (or any) boarding me in phase 3.