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Beat him a few minutes ago with two mk II burst lasers and an ion mk II, took him out with ease by rapid-fire ionning his shields, lasering the rockets and drones (when active) the hitting the shields. Unstoppable until phase three where he actually got a good bit of damage on me.

Notable systems:
Four shields
Level three arty beam
Level two oxy
Maxed out doors
High level engines (Not max)
No augments

Crew:
Pilot: two stars, human
Shields: two/one star, engi
Weapons: two star, mantis
Engines: two star, rockman
Reserves: two rockmen, one human, one engi

Weapons:
Burst laser mark II x2
Ion blast mark II

Ship: Federation cruiser, type A.

I think I did pretty good as I only meant to reach rock homeworlds to get the ship and having three encounters with the rebel fleet in a row (though the quest that caused me to lag behind them gave me the ion), but after it wasn't there and I had such a powerful armament I kept going, good call I think.

strange wrote:(... spam ...)

Wait, What? Thats seriously off topic!
Well, it took 7 tries to beat the flagship. and once i did, won 2 times in a row.
First victory was with the human ship, had:
Burst laser MK I
Breach bomb MK II
Fire bomb
And something else i dont remember.
i used 4 point shield, 8 bars.
almost maxed engines
teleporter and cloak
Second time with the federation cruiser. Had:
Burst laser MK I X2
Fire bomb
Ion bomb
Ioned the shield while the BLs Did the job.
Also 4 point shield, and teleporter, almost maxed engines, but with no cloak.

I could've beated it without cloak really, Vortex on Normal. With an only lv3 shield. Combination of 1) Defense I and Defense II drones, and 2) Using lasers to destroy at least one drone during the drone swarm (Actually did it three times instead of cloaking, for the lolz).

On an easy Kestrel run, I killed all the crew in the first stage with Crystenant and his three Commantis. Didn't have any problem on the next stages either: I ended up losing less than 25% hull in all three fights combined. At the third stage, and also for the lulz, I set the whole ship on fire with my fire beam, getting that achievement. Then I fired a laser and ended it, can't remember the model, but I had two powered Ion momb teleporters that weren't fired for for the whole time.

Well I won the thing with a Red-Tail, unknown gear layout with 3 mantis and 1 rock as boarders and at least 2 heavy lasers mark 2 (i remember firing them in sync, think i also had some sort of burst laser).

1. Beam my elite team (dual mantis, one of them the legendary Mantis thief KazaaakplethKilik ) into missile bay.
2. Beam my vet team (mantis-rock) into ion cannon.
3. Take the fire while waiting for the first team to do something. I think. Note that during the entire fight, you must pause the game whenever the mothership fires the missiles (or later ion cannons, also note that I'm assuming a build including level 2 stealth or better and a quad shield)
4. Beam the elites out and into the laser cannon.
5. Beam the vets into the beam array.
6. Once all weapons are toast, use a quick burst (always make sure your heavy lasers fire AFTER the last shot of the light lasers, and make sure all guns are charged and ready, half-volleys like the AI tends to do won't work) against their shield generator, giving you some time to take out their cloak.
7. Blow their cloak out.
8. Wait until an appropriate amount of the mothership's crew is in the cloaking room (and door room if possible), open fire at the cloak.
9. Enjoy the sight of having killed from 3 to 5 of the crew.
10. Repair your ship and jump to the next battle.

This one was a bit trickier due to the drones, but the stealth should take care of the power surges. Make sure you only trigger them once they start shooting, not when you receive the warning. Otherwise you've wasted most of your stealth for nothing.

1. Beam elites into missile bay.
2. Beam vets into laser cannons.
3. Use controlled bursts to take the drone controls out as soon as you can - preferably between steps 1 and 2, possibly sooner.
4. Beam elites into beam array.
5. Beam vets out, if desired you may attempt to grab some attention to keep the drone controls offline.
6. Once beam array is offline, destroy ship by firing at drone controls. WARNING: Make sure that all but 1 of the mothership's crew are dead (got lucky by starting a fire in the drone bay, kept them offline for the duration of the battle) by luring any survivors into the drone control room. Failure to do so will result in the following:
A: Mothership will become an AI. Presumably very bad, but I haven't experienced it.
B: You will have left some of them alive, forcing you to deal with boarders in stage 3. Assuming you did stage 1 properly, that's not necessarily a bad thing as it lets your boarding teams do something productive after destroying the weapons, which you may be able to knock out without them.
7. Fix up, jump to stage 3.

This is a cakewalk if you did the previous stages right. Just keep the shields offline and watch for that power surge.

1. Take out zoltan shield.
2a. Beam elites into missile bay, beam vets into laser cannon.
2b. Fire all weapons at the enemy weapon systems, emphasis on destroying missile launchers.
3. Disable enemy shield generator. This will allow you to deal damage without having to time your volleys efficiently.
4. Well, blow them up already! Note that if the mothership should do a power surge, your only escape is to cloak. As in stage 2, wait until it actually gets into the "I'll deal some damage if you don't cloak RIGHT NOW" phase, or in other words, fires the barrage.
5. Enjoy!

Oh, by the way, 2b is more likely to work if you failed to get rid of all (except 1) of the enemy crew.

I don't get why people think that fighting an ai ship is difficult or why people use such big boarding crews. A single mantis is enough to take down the weapons. Yes, you do take some damage but if you can't handle such a small amount of damage I don't know how you managed to get this far. I took out the mothership 3 times already. Twice with the kestral I believe(first time with only an ion and 2 damage laser as notable weapons, don't remember the second time weapons but it was boarding based with only 2 boarders) and once with the ship you get for winning(oke, I did have a burst laser mk 2 and 3 and a beam and fully upgraded special weapon but used only 1 mantis to board). And fighting an ai ship is almost easier then fighting a ship with crew. Just send 1 crew member to every system you want destroyed and call them back(or not) before destroying the ship. The ship can repair as much as it wants but it won't help.
p.s. Yes, it was on easy but that only makes a difference in the random fights.

While this is an excellent guide, don't lose hope if you get to the end without what is perscribed. There is still hope with other set-ups which I learned on my first Normal victory.

No Cloak, No Teleporter, and even missing a few reactor blocks. 5 on the engine, 2X2 on shields,
weapons: burst laser II, heavy laser I, Artemis, and ion blast II
drones: defense II (4 energy)
and two capacity on most other systems (though only 1 on the medic system).

According to best strategy, this isn't the ideal setup, but it proved just enough to take the flagship. I healed between battles 1 & 2, but with no chance between 2 & 3, it was tense and ended with about 6 points left on the hull. Also, all enemy crew members but one died trying to rush the ship, which helped in the last battle (I had 8 crew, including 2 rockmen but no mantises).

The basic strategy was to hold the heavy laser so it could fire in tandem with the burst laser until the shields were weak enough. Then I generally attacked the weapons, with special focus on the two front weapons, successfully killing the crew in those stations in the first and second sections.

Just wanted to share that while the boarding and\or missile strategies are ideal, some combinations have a hope without it.

headcase wrote:While this is an excellent guide, don't lose hope if you get to the end without what is perscribed. There is still hope with other set-ups which I learned on my first Normal victory.

No Cloak, No Teleporter, and even missing a few reactor blocks. 5 on the engine, 2X2 on shields,
weapons: burst laser II, heavy laser I, Artemis, and ion blast II
drones: defense II (4 energy)
and two capacity on most other systems (though only 1 on the medic system).

According to best strategy, this isn't the ideal setup, but it proved just enough to take the flagship. I healed between battles 1 & 2, but with no chance between 2 & 3, it was tense and ended with about 6 points left on the hull. Also, all enemy crew members but one died trying to rush the ship, which helped in the last battle (I had 8 crew, including 2 rockmen but no mantises).

The basic strategy was to hold the heavy laser so it could fire in tandem with the burst laser until the shields were weak enough. Then I generally attacked the weapons, with special focus on the two front weapons, successfully killing the crew in those stations in the first and second sections.

Just wanted to share that while the boarding and\or missile strategies are ideal, some combinations have a hope without it.

Indeed. I just did it about 15 minutes ago in a Rock B cruiser, 2 Zoltans, 5 Rocks, 1 Crystal, maxed beamer, maxed medbay, maxed sensors, maxed engines, maxed shields, maxed(?) weapons (but not really optimal performance out of that stuff), starting weapons, Burst Laser 2, Halberd Beam (very sparsely used, sadly), no cloak, anti-ship drone 1, system repair drone, and maxed life support.

Frankly, I took quite a beating. And it wasn't even when you'd expect it, in stage 2, but rather in stage 3 due to not having the ability to cloak before the laser burst.

1. Follow steps 1, 2, 3, 4, and 5 from my previous post.
2. Beam your crystal and rock into cloak after launching a fire bomb. If you did it right, you will only be fighting 2 inferior humans with plenty of time to beam out safely.
3. After beaming them out and healing them, repeat the process in the enemy life support system, minus the fire bomb.
4. If necessary, repeat step 3 in another densely populated zone until there is only one man alive.
5. Destroy the ship, making sure the last crewman is not killed in the process.
6. Perform maintenance as needed.

Next stage was actually a lot easier than I expected, though the boarding drone went straight into my engine room causing minor problems.

1. Follow steps 1, 2, 3, 4, 5, 6, and 7 from my previous post regarding stage 2, but try not to kill the surviving crewman.

And this was the tricky bit. Lacking a cloak, I found it extremely difficult to withstand the power surges.

1. Follow steps 1, 2a, and 3 from my previous post about stage 3. Note that you may find boarding the weapons unnecessary, and that boarding the shield generator is very useful if playing with a gear layout such as my own, making it very hard to penetrate a quad shield. Again, do not kill the crewman.

Edit: True now, the post I quoted was MUCH worse off, and I was playing Easy, but... still a bit worse than my previous victory. In fact, I was genuinely concerned in stage 3, my hull couldn't have been above 10 by then.

I think I lucked out with the final boss.

Phase 1: teleport 2 crews around to destroy the isolated guns. Then, bomb the sickbay and plant 2 rockmen in it. Keep using the healing bomb on them until it's done.

Phase 2: again, teleport the 2 crews around to kill the guns and the droid systems. I didn't know you could cloak through the power surges at this point.

Phase 3: the ship's an AI but it does have air. Wreck everything as in phase 2. I graciously noted you could cloak through the super attacks at this point.

I...don't know if the fight bugged or something? I don't remember it all that clearly, but...I kinda kicked his ass.

Kestrel w/ 2 Burst Laser Mrk 2, Artemis Missile Launcher, Heavy Laser

Drone Control w/ Defense Drone, max shields, lvl 5 engines, NO stealth, NO teleporter, 2 weapon cooldown accelerator mods (I forget what they're called)

4 humans, 1 slug, 2 mantis, 1 zoltan, 1 engi (all stations manned at lvl 2)

Knowing nothing about the boss fight going into it, all I did was focus down the ion cannon first, then shields, then lasers. I didn't go after the missiles because I figured the defense drone made them less dangerous then the lasers. I don't think my shields ever went all the way down, so I just had to run around the engi and the repair-focused human to take care of the occasional missile damage.

I...didn't notice the power surge attack. I noticed a lot more drones in the second stage, so I did focus down the drone control, but...maybe I took them out before the power surge? Third stage, I got boarded by a couple things, I thought they were drones, I could have been wrong.

My best guess is that, between the 6-shot volleys and the artemis missiles, with +49% weapon recharge rate from lvl 2 crew and 2 mods, I just managed to tear him apart before power surges. Failing that, all I can think of is that a 45% dodge rate marginalized their effectiveness to the point where I didn't notice.

Or the fight was bugged. I'm really not sure which is the more likely explanation.

the first time i beat it was with the Torus ship with this setup:
2 Ion Burst Mk2
1 Burst Laser Mk2
2 Anti-Ship drone Mk1
1 Beam drone Mk1
Lv1 Cloaking
3 Shields active
4 Engines
With a crew of 3 Engis and 1 Human

I just spammed Ion the shield then my drones did the rest of the work