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12 runs, 11 hours, all runs on Easy and I still haven't beaten the flagship. I shall share the tale of my previous run.

After a rocky start - by which I mean my Kestrel A, the Ascendant, went below 1/4th of its hull strength in the first three jumps - I was doing pretty well. A Glaive Beam was just floating in space, so I took it. I had to sell the Artemis to get the power for it (good riddance, I hate using missile weapons), but it was devestating once I could use it and my Burst Laser II. Like all smart beam users, I used the Burst Laser II to take down shields, then used the Glaive Beam on as many rooms as possible. And this went well! In Sector 7, I found another Burst Laser II in a store, and instantly bought it - two Burst Laser IIs is a strong loadout on its own, but with the help of a Glaive Beam? Absurdly powerful! The race was on to get those last 2 weapon power upgrades (literally the last two - if I were to have two Burst Laser IIs and a Glaive Beam, then find something else, I would have to ditch a weapon because it will not let you have more power than required for those three weapons) before reaching the flagship, and some more reactor power so that I could actually use it. And at some point I found a Weapon Pre-Igniter, which was incredibly helpful in avoiding damage, and reduced frustration while waiting for the Glaive Beam to charge (it's a wonderful weapon, but so very slow).

I had one out of the two desperately needed weapon upgrades, had reached the final sector, and suddenly, the game decided to break out the missiles now that I actually needed more scrap. I had to jump away from several rebel ships to avoid destruction, and accidentally accepted a surrender in one of the few fights I won, preventing me from buying the much-needed upgrade (nine scrap more and I'd have had my second Burst Laser II).

I was one jump away from the flagship, which was only two jumps away from the base, so I decided to just go for it and hope that 2 damage per room was enough.

This did not end well.

I started out fairly strong, taking down three shields and guiding the Glaive Beam across some of the deadlier weapons (THAT BLOODY MISSILE LAUNCHER...). I repeated this, attempting to kill the gunner of the launcher so that it would not be repaired, and things started to go wrong.

The RNG had apparently decided that it was no longer my friend, and started making all of my Burst Laser II shots miss. This prevented me from being able to keep the deadliest weapons nonfunctional. Of course, my dodge stat - which I'm fairly certain was 45%, was not helped in any way, and most of the flagship's shots hit.

First my shields went down, so I could no longer rely on the flagship gunners' apparent lack of communication to cause the beams to hit first, then the heavy lasers, then the ion cannons to hit, preventing a large amount of damage. Then my weapons went down, removing any chance I had of killing it, as I only had three shots, completely incapable of getting through a 4-layered shield like the flagship has. From there, things continued to spiral downhill until the Ascendant finally exploded violently.

Still, I did an entire 8 damage to it! Beats my previous record of 0 damage.

Took me about 40 games personally.

To the game's discredit you need a very specific set up to defeat the final boss. The only thing to really note is that the boss has 2 very distinct weaknesses:

1. Weapons are completely cut off from the rest of the ship. When attacking weapons via teleport or just normal weapons no one is coming to help the gunner or repair the weapons.

2. The crew. The boss recharges everything between fights except it's crew. Once a crew member is dead, they're dead. However if you kill everyone an AI takes over and starts repairing everything which is bad. The usual strategy is to leave the gunner of laser weapons alive to avoid this, as the laser and missiles last until the last phase. However the boss becomes a bit easier when nothing is manned. (esp. the dodge rate)

Ideal:

Drones: 1 defense I drone. (Defense II gets distracted by lasers, you just want it to protect you from missiles and boarding drones. 2 defense I drones should protect you from all three missiles from the bosses missile launcher)

Cloak: Best way to dodge volleys is just cloak through them. In phase 2 & 3 watch for the "enemy power surge" warning to know when best to cloak.

Weapons: Bombs or Ion Blast II. Ion Blast II has such a short cooldown that if you keep it firing on the shields it will keep the bosses shield down indefinitely. Bombs are the second best thing to get through shields and it also kills enemy crew.

Teleporter: Best way to destroy weapons is to teleport in an destroy them, starting with missiles. Just send two people or one good fighter (rock/mantis) and that will be enough to overwhelm the one gunner.

Everything else: 3 shields, 5 engine, 3 doors, 2 sensors.

Augments: Weapons Reloader, Shield Recharger, and Stealth Weapons are ideal.

i won after losing exactly 50 times.
my first few games were decent, i think i got to about the fifth sector consistently, and i unlocked the Torus relatively early. So i tried it out immediately but i didn't really like it. I thought it was really annoying that it used up drone parts as it's main fighting style (i am also one of those guys who walks around with 100 health potions in rpgs because it's a waste to use them when you don't absolutely need them, and when i realize i do i am already dead). I also didn't like the fact that ion weapons didn't do any damage. So i ended up trying to get my Torus to get damage weapons and not using it's drone system. It didn't go well and i soon went back to the trusty Kestrel. i later unlocked the Zoltan and Stealth cruisers. The Zoltan was usable but still not as good as the Kestrel and the Stealth cruiser was incredibly hard to use, as i needed to spend alot of scrap on repairs while still saving for the shield system. eventually i unlocked the Red-Tail which was about as good as the regular Kestrel too me, and i kept swapping between the two and sometimes one of the others too. By this time i had encountered the boss a few times on easy, but never even beaten the first part. So i looked up a guide on the internet, saying that teleporters are the way to go. I hadn't really used the teleporter before but i now discovered that it was actually pretty useful, especially because you get much more scrap. The next few runs (or the runs in which i made it to the boss) i used the teleporter to kill of the gunners except the laser guy. Most of the times this worked, although my melee soldiers did die some of those times. But i always died when trying to fight the second stage. I eventually got back to trying the engi, and after only one game discovered that ion is actually really usefull, especially due to the speed of the mark II. I also found that the drones could be really powerful, especially with the drone recovery arm. And so it was that at my second run rediscovering the Torus i beat the boss using two mark II ions, a two shot laser weapon, fully upgraded shields and weapon systems, full subsystems, anti ship drone I defense drone I and an anti-personell drone.
It's kind of funny how the ship i at first absolutely hated was also the one that got me my first victory.
51 games played, 1 game won.

I met the boss after about 20 tries. I haven't beaten him yet.

I refuse to look up strategy guides until I win it on easy at least once.

today is the 13th of January. today was my 13th run on easy and I won, for the first time. this calls for a celebration, that is this post, yay! this win was sponsored by the Torus and lvl 3 cloak. now for a test run with the Osprey...

Not going to lie, it was something like fifteen-twenty times, and I had fixated on beating with the Kestrel before moving on. Naturally, the first time I win, everything seriously went my way, I remember - turning away crew members, a fire beam just dropped in my lap, I unlocked the stealth cruiser on the same run.

I think my four runs after that didn't make it past sector 3, of course.

I won on my 41st attempt. On Easy. I started playing the game on normal for about the first 6 games. This did not go well, and I switched to Easy. The game previous to the one I won, I got to stage 3 of the boss ship using 3 basic lasers and an ion weapon, 2 defense drone I, and a teleporter. I couldn't find any weapons that run. The game I won, I was incredibly lucky and went into sector 8 with 3 Burst Laser Mark II and a Hull Beam. No cloak, teleporter, or defense drones. I figure the boss ship would kill me without any missile defense, but my weapon loadout just shredded everything including the Boss. Nothing quite like 9 laser beams hitting simultaniously. I am totally addicted to this game. It plays differently every time based on what upgrades become available to you.