Final Boss Guide (Spoilers)

[GhoXen]

General
If the text on the star chart isn't clear enough, the final boss will slowly jump from beacon to beacon towards the Base. There will be a lot of free repair stations in the system, and they are reusable (i.e. use "Wait" at a repair beacon will repair you again). At the same time the rebel fleet will start claiming various beacons. You have to destroy the Flagship three times before it reaches the Base. You can repair between fights, assuming the rebel fleet hasn't taken over the repair beacons.

A few things you will really want: maxed out shield, level 4 engine (anything more and you probably won't have power for it), at least rank 2 stealth, either a level 3 teleporter with lots of mantis OR a lot of firepower/bombs/missiles/ion.

First Stage
The first fight may be intimidating, but it's a fairly traditional fight. The boss has four weapons, each with its own system. From left to right, they are ion burst (3 shots), laser burst (3 shots), missile burst (3 shots) and a beam weapon. The systems for the four weapons are manned by a single crew each, and are not connected to the main body, so the rest of the crew can't help or fix the system. The ship has 4 shields, a very large crew (who will not board your ship in this stage), and a stealth system. Obviously the first things you want to take down are the missile and ion.

Boarding-focused
If your ship is heavily invested in boarding, then the first thing you want to do is to teleport 2 of your mantis to the weapon system for the missile burst, and then another 2 to the ion burst. Once the systems are destroyed, teleport your mantis back, take out beam, DO NOT touch the laser weapon. Make sure that the crew manning the laser weapon remains alive. You'll see why soon.

Now focus on the rest of the ship. The goal is to kill the entire crew except the lone guy manning laser. You should use bomb/missile to destroy the med station on the ship, teleport your mantis in, and teleport them back at low health. IMPORTANT: while the Flagship is in stealth, you will not be able to teleport your crew back, so you may want to destroy the stealth system as well. Keep on teleporting back and forth, keeping their med and stealth down. Level 3 teleporter will be essential here, and the healing bomb can be very helpful.

Once the entire crew is dead, except that one lone guy, proceed to destroy the shield from within and the hull. The reason that you must leave one crew alive is because a) although the ship repairs its systems between Stages, the crew carries forward; b) if the entire crew is dead, the ship becomes an AI ship, and all systems automatically repair themselves, the subsequent fights will become nearly impossible.

Weapon-focused
If your ship is heavily invested in weapons, then I hope you will have either a lot of good missiles/bombs or a lot of ion weapons. If you have two Ion Blasters (especially Mk2 ones), autofire those on the shield and the ship's shield should be locked down within a few second. Proceed to destroy missile weapon, the ion weapon and the beam. Make sure that the laser remains untouched, the crew manning the laser must be alive. Alternatively just spam missiles/bombs at the three weapons until the weapons and the crew are both down.

Once the ship is mostly harmless, proceed to kill the rest of the crew, except the one person manning the laser. I recommend breaking the medbay, set it on fire, breach its hull, use small bombs and watch the crew rushing to it one by one to be roasted. The reason that you must leave one crew alive is because a) although the ship repairs its systems between Stages, the crew carries forward; b) if the entire crew is dead, the ship becomes an AI ship, and all systems automatically repair themselves, the subsequent fights will become very annoying. When all has been done, destroy the shield and hull. Don't use too many missiles, you'll want a good stash for the next two fights.

Second Stage
In this stage the ship will lose its stealth system and ion weapon. All other systems will be repaired to full, but the crew will remain the same. If you've done everything correctly, then there should only be one poor sucker manning a laser, trapped between 2 squares. This time around the boss will focus on droids. The boss will send boarding droids onto your ship. Don't bother killing them, the boss will just send another one if it's dead. There will also be a new mechanic called "Power Surge". When a "Power Surge" is happening you will receive a warning similar to solar flares. In this stage the Power Surge comes in the form of 10+ anti-ship/beam droids spawning and ripping your ship apart. Power Surge droids will spawn and function even if the flagship's droid control system is down.

Boarding-focused
Send 2 mantis to the droid control system and 2 mantis to the rocket. Ideally your ship should at least have a few doors to keep the droid occupied while the systems are being damaged. Once the rockets are down, and the droid control is damaged enough for the boarding droid to go offline, head to the shields and engines. Tear those apart and the ship will be fully defenseless.

While your boarding crew is working, your ship needs to survive the Power Surges. The spawned droids will last awhile, so you will want to time it carefully. Don't hit stealth as soon as the warning shows up, instead you should only stealth when you see the spawned droids starting to fire. Level 3 stealth will of course make things easier.

Weapon-focused
Pretty much copy-paste First Stage strat. Ion-weapon lockdown shield, destroy droid control and rocket, or use missiles/bombs. The more important part is to survive Power Surges. You will want to time it carefully, since the spawned droids last awhile. Don't hit stealth as soon as the warning shows up, instead you should only stealth when you see the spawned droids starting to fire. Level 3 stealth will of course make things easier.

Third Stage
In this stage the ship will lose its droid controls and the beam weapon. In this stage the ship will now have a somewhat powerful Zoltan shield, and start migrating its entire crew onto your ship. Fortunately they are all dead, except that one guy who can't reach the teleporter anyway. The Power Surge in this stage comes in two forms: it will either fully restore the Zoltan shield, or it will send out a barrage of lasers at your ship (around 10 bolts).

Boarding-focused
Throw everything you have at that damn shield. If you don't already know by this point, you can't teleport into a ship while the Zoltan shield is active. Once the green shield is down, teleport your mantis to the rocket and destroy it, then to the shield and engine.

The Power Surge is easier to dodge than Second Stage because it doesn't last nearly as long. Even rank 1 Stealth should be sufficient. Again, time it when you see the barrage of beams firing, not when you see the warning. Indeed, you may not want to use high ranking Stealth at all. Since those stealth last too long, their cooldowns start later than rank 1 and you may not have stealth available when the next wave of lasers are coming.

Weapon-focused
I guess it's starting to become rather obvious that Ion-lockdown is pretty OP. Do that to the shield again, then destroy rocket and engine.

The Power Surge is easier to dodge than Second Stage because it doesn't last nearly as long. Even rank 1 Stealth should be sufficient. Again, time it when you see the barrage of beams firing, not when you see the warning. Indeed, you may not want to use high ranking Stealth at all. Since those stealth last too long, their cooldowns start later than rank 1 and you may not have stealth available when the next wave of lasers are coming.

Conclusion
Per design Stage 3 is supposed to be the hardest. Indeed on my first playthrough where there was poor planning, my ship was quickly overran by 8-10 boarders tearing my ship apart from the inside. With knowledge of the fight and proper planning, the final boss is arguably easier than some dice-blessed enemies you may run into (i.e. mantis ship vs autoship with 4 shield and rockets).

PS: Will add pretty pictures later.

[movingtarget]

i took him out in a torus armed with 1 ion blast 2 1 ion blast 1 and a fire beam, just drop the shields and lit it on fire , also made alot of salvage capturing enemy ships with this config even rock man ship, my tactic threre invovles lighting the o2 room on fire

[Jeden]

I beat him moments ago, I had the Zoltan ship B. I kept the initial two ion cannon MK 1's and the Pike beam, and added a second pike cannon. I also had a max cloak (don't need the full 15 seconds, but allows it to take several hits), max engines (48% evade), max shields, and drone command with an anti-personnel drone and a repair drone. Also, and this is important, max doors. Those doors will save your ass, they seriously slow down enemy boarders and stop your crew suffocating to death until the repair drone was able to fix the leaks.
Augmentations: I sold the Zoltan shield, and got a pre-igniter, and rapid reloader, and an ion reverser (or whatever its called, reduced ion damage and 20% chance to negate entirely).

My basic strategy was to immediately set the ion cannons to beat up the shields on autofire. I had level 1 cloak active, and when he fired the missiles I cloaked so they missed me. This meant that he was basically unable to hurt me; most of the lasers missed, the ion was ineffective and the beam couldn't pierce my shields. Once the shields went down, I set the pike beams on auto fire so they crossed as many rooms as possible, always including the shields. This meant that once the shields were down, they stayed down.
Only strategy changes for rounds 2 & 3:
Round 2:
cloak level 2, cloaked whenever the power surge occured, and if possible when the boarding drones were on their way. Rinse and repeat shooting from stage 1. This is probably the most challenging stage, I only had 4 crew so I really relied on the repair drone and anti-boarding drone, as they're essentially immortal as long as you have enough drone parts.
Round 3:
Cloak 2, cloak on power surge, send anti-boarding drone to teleport boarders. If possible, vent the areas to vacuum, the drone doesn't need air but boarders do. Just keep beating on it and cloaking and it goes down like Liston.

[manyallaluk]

I found the boss to be a cake walk with the Torus type A.

Weapons: ion blast II, a burst laser, and missiles (I think the ion blast was most important)
Drones: 3 laser drones II, 1 repair drone in storage
Augs: salvage, nano-healing, and drone collector
Crew: 2 Engi, 1 slug, 2 Zoltan, 1 Humans, 1 Rockman.

I think my shields were max, as well as doors, and med-bay.

Basically the drones and the ion blast would take down the shields and the other weapons plus stray fire from the drones would do the damage. More ion guns probably would have helped. The Drones constant fire kept the shields down for the entire fight. Once a round was finished I could use a repair drone to fix the hull and I could just go strait into another fight without going to a repair station.

[GoldenShadowGS]

What difficulty?

[Thidran]

Beat the game with the Kestrel.

My crew: 4x human, 1x crystal, 1x rockman, 2x engi. (The stations had learned folk on each to boot).

My weapons: 3x burst laser mrk 2, 1x Glaive beam(which I didn't bother using).

My drones: anti-ship I

My strategy: Beat the hell out of the opposition by laser beam spam, focusing down the 4x shield by 9 shots each volley. Whenever his weapons were firing, I'd cloak asap(had level 1, upgraded to 2 by the third form). Third form was a gambit. Even with the anti-ship, I barely made it. My ship ended up being a glass cannon. The boarding actions were pathetic though. My extra units just beat the stuffing out of each attempt to board.

[LNQ]

Has anyone tried to kill the crew on the flagship? Can you win in phase 1 if you kill the crew?

[Vurogj]

Has anyone tried to kill the crew on the flagship? Can you win in phase 1 if you kill the crew?

This is covered in the first post. The flgaship becomes an auto-ship if the crew dies.

[AyameCroc]

Just beat him a few seconds ago.

My layout was on the Red Tail.

Weaponry: 1x Heavy Laser, 2x Basic Laser, 1xBurst Laser III
Drones: Defense Drone II
3x Zoltan, 1xMantis, 1xRock, 1xEngi, 2xHuman

I made it all the way to sector 8 without changing weaponry at all, so once I got there I knew I had to spend on getting the weaponry up and getting more than just 4 basics as that wouldn't be enough to break the shield and then keep it down.

As soon as he de-cloaked I teleported the Rock and Mantis in and took out the weaponry one by one whilst battering the shield as much as possible, Once the shield was down I let him decloak and kept the shield down giving a little time to teleport my guys back in to the Piloting room. With the shield down I took out the Medical Bay being careful I didn't deal enough damage for the whole thing to go.

I then destroyed the ship with just two guys left. The next two stages were easy as it just involved taking down the shield and then drone room (tele in again whilst hitting the shield). The final stage was a easy enough once both weapons had been taken down and I got the timing of cloaking down.

\o/

[BoardroomHero]

Has anyone had luck without stealth?

Every time I go against him with stealth, the fight doesn't tend to be that hard. If I don't have stealth, I get crushed on the second stage. Those drones are more than enough to tear through rank 4 shields, and the beams will hit enough systems before shields come back on to make recovery near impossible.