Final Boss Guide (Spoilers)

[Peo01]

I destroyed the flagship without cloak.
Used a combination of heavy firepower, boarding parties and defense drones.

Although it was easy to destroy it with that strategy on easy it was pretty close on normal.

Can't remember all the equipment I had (I remember having long range sensors and shield recharger).
Weapons used:
Burst Laser II
Heavy Laser II
Halberd beam
Hermes missles
Drones:
Defense II
Beam I

Here's a (bad quality) video of the fight:
http://www.youtube.com/watch?v=-h2fUvFjqZ4

[Maya]

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.

You need to take out his Drone control system, this way he just can get through 3 Bubble and the 4th saves your live^^. But ensure that you take out his Beam and Rocketstation in the First stage to ensure, that he won't ignore your Shield and you shouldn't make him an AI ship, cause then it get's even harder to win^^

[GhoXen]

What difficulty?

Applicable for both difficulties. I didn't notice any difference in the fights on Easy and Normal. The only difference is that you get more scrap on Easy, so you may have better weapons and upgrades than on Normal.

[GhoXen]

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.

You need to take out his Drone control system, this way he just can get through 3 Bubble and the 4th saves your live^^. But ensure that you take out his Beam and Rocketstation in the First stage to ensure, that he won't ignore your Shield and you shouldn't make him an AI ship, cause then it get's even harder to win^^

The power surge droids will still spawn and function even if the droid control system is down. However the boarding droid, and the persistent anti-ship and beam droid will cease to function, which will certainly cut you some slack.

On one of my playthroughs I managed to beat the boss without stealth using a very heavy firepower ship (Ion Blast II, Ion Blast II, Burst Laser II, Anti-ship drone I, Anti-ship drone I, along with rank 3 Artillery Laser). I was able to completely destroy the hull before the first power surge even finished, but I still took some damage.

[Flickey]

I beat the boss without stealth. Got my engines up for 40+ percent dodge chance and had quite some firepower (2 MK2s, one basic laser, one heavy laser). P2 drone surge was no problem at all with 3 shield points, not sure why (dodge?). I used one MKI def drone. Normal difficulty.

[DasRav]

Beat it last night with the Kestral A. I had a epic 2 mantis boarding party with yellow combat skills, but those blew up in the last fight before the boss due to me missmanaging my lasers, so I was basically looking to suicide into the enemy. But then I won

I had 2 Hull lasers mk2 and a fire bomb. Firebomb was VERY epic in killing the enemy crew and shield and with the hull lasers I just devastated their hull once the shield was down. Stealth obviously also came in handy for stage 2. By stage 3 everyone on the enemy ship had burned to death and I faced the AI ship and burned that too, with 3 health left on my ship. Far from the optimal strategy, but it somehow worked.

[GoldenShadowGS]

I finally beat the Boss with the Red Tail, (Kestrel B) I had a breach bomb, ion burst 2, basic laser, basic laser. Hull repair drone, defense drone 1. I had about 6 missiles and 20 drones. 7 crew, maxed out for their stations.
My shields were only 3, but my engines were very powerful, I had 51% evade with my maxed pilot and engine operator. I sent my boarding team to take out the 1st, 3rd, and 4th weapon rooms, then I sent them to attack the helm, as they did, I sent breach bombs to the medbay which killed the people trying to heal. Its actually a good strategy. The low health guys will not run to the medbay if it is broken and has no air in it. So, I only needed a couple of teleport cycles until everyone was dead. I used my crew to keep my ship is working order and topped off my HP with a hull repair drone after I defeated the first phase.

Jump to the next phase, I sent my boarding team to the missile bay and disabled it, then the beam weapon bay. After that, I took out the drone bay, then helm and shields and then finished it off with basic lasers.

For the third phase, same drill. Take out the missiles, then helm, then shields and finish it with basic lasers. That hull repair drone is a life safer. Try to get at least 2 bars in every sub/system too.

[Arqane]

Fun to read all the other strategies for the fight, seeing as mine was so simple. Alpha strike. Weapon Pre-loader, good weapons (I didn't have a perfect layout either time), and target everything on the shields. So far the strategy is 2/2 and quite easy. Neither ship had stealth, neither really used boarding parties.

My first victory was in the Red-Tail. I had a Burst Laser 3, Burst Laser 2, Heavy Laser 1, and Breach missile. I won part 1 with the BL 3 and Breach missile mainly, but it was a little slow. I sent in a boarding party of 2, but I did something silly that I forgot, and both died quickly without doing much. Part 2 and 3 I switched to the 3 lasers, and just focused on the shields. That was it... no other tactics, no defense besides 4 shields.

My second victory was playing with the Osprey I got after beating it the first time. Same tactic, only this time I had two Burst Laser 2s and a Hull Laser 2, as well as a fully upgraded artillery beam. By now I had the alpha strike tactic down to an art! I shot all the lasers at the shields at the beginning, then kept doing that. This time I only had L3 shields, a defense drone 1, and a whopping 27% evade, but it still worked out the same way.

So that's it. You don't really need ion or stealth. Or tactics for that matter, other than making sure you go for the shields to get a lot more damage output. I'm not even sure I really needed a pre-loader for this, but it doesn't hurt.

[DSchrute06]

FINALLY I beat the Boss with ease. I've made probably 20-25 runs on easy, and save for one time beating "him" by the skin of my teeth, I've failed every other time. Tonight was different, I not only beat him, I annihilated him. I never lost more than 5-6 bars on my power bar in any of the three stages. Here's what I had:

2x - Burst Laser III
1 - Breach II self teleporting bomb
1 - Anti-Ship Drone
1 - Hull Repair Drone

I was using The Osprey so I also had the Artillary Beam, obviously, and I had it maxed. I didn't have cloaking and I only had three shields. I had the augmentation that has each of your weapons ready to shoot immediately after each jump, that helped quite a bit.

I started out immediately using Breach II on the missile cluster second from the right. I spaced my two Burst Lasers out by a second or two and then put everything on auto shoot. It took two or three Breach bombs to take out the missile cluster and the crewman assigned to it. By that time the ship cloaked again and I immediately disabled my Anti-Ship drone and activated the Hull Repair drone. I did this once or twice more as the ship cloaked and that easily made up for any power bars I lost during the fight.

After the missile cluster was taken care of I took out the laser to the right of it with the Breach bomb. I also moved both of my Burst Lasers onto it to make sure I took it out nice and quick. With one Breach bomb, my two Burst Lasers and my re-activated Anti Ship Drone I easily took out the remaining shield and finished off the laser in the next round of firings. At this point my Artillery Beam had reduced the first stage to just another couple of shots and it was finished.

The other two stages went exactly the same, I started out by taking out the missile cluster, took out the remaining weapons after that, and activated the Hull Repair drone when needed.

One thing did confuse me in stage 2. After taking out the missile cluster and crewman guarding it (I had upgraded sensors so I'm positive both were finished), a few seconds later the missile symbol changed from red back to orange as if it had been repaired. I'm not sure how that was possible considering each weapon area is blocked off from the rest of the ship. A glitch maybe? Who knows, it didn't bother me because it didn't matter...before it had a chance to shoot again my Artillery Beam and another round of Burst Lasers made short work of the stage.

I've read opinions, on this forum and others, that it's next to impossible to beat the ending without cloaking. I just wanted to stop by and say that it's not at all if you have the right combination of equipment. The Hull Repair drone was more than enough to make up for the damage I suffered from various attacks, including the drone swarm in part 2, and remember I only had three shields on top of zero cloaking. The only problem I see with this game is that a lot of it depends on what you're able to find, and since you don't really control that there's an element of pure luck involved which I've never been a fan of. Some of my runs I had literally zero chance, I just didn't find the right combination of weapons that could do what I needed.

[nimitz98]

W00T! I just now beat the Flagship with the Torus! I had the original Mark II Ion, a Heavy Laser I, a Pike Beam, a Mark I Anti-Ship drone, a Mark I Defense drone, an Anti-Boarding drone, and a Teleporter. For the first stage, I set up my drones, laser and ion to beat up his shields on auto, and sent my Enigi and Slug to his weapons. Once his laser, ion, and missiles were destroyed he was defenseless, and after about 10 minutes of constant firing my weapons broke through his shields and I ripped him apart with my pike beam. I was sure I was going to be destroyed by the drones in the second stage, but my shields held and my anti-boarding drone held off the intruders. My weapons soon broke through the shields, and again, I shredded him with mah awesome pike beam. The third stage was a cakewalk. Took out his missiles, broke through his shields, and cut him to pieces.