How can I beat the final boss in faster than light? I can beat the first form, but the second form just obliterates me regardless what I try.

I have tried using nothing but missiles, a combination of every single weapon I can find, and stealth. I have not tried using drones because of the amount of scrap and luck of the draw it takes to get them up and running on the stock ship. I have also been playing on easy.

  • Well, what have you tried? And are you playing on easy?
    – Frank
    Aug 19, 2012 at 22:40
  • 1
    @fbueckert updated to include what I have tried.
    – Halfwarr
    Aug 19, 2012 at 23:19
  • I have beaten the boss with engi ship: 6 crew, attack and Def & drone MK1, the starting weapon, the missile that breaches the Hull. 4shieds, alot of engine upg, cloak but no cloak weapons.
    – BlueTrin
    Nov 16, 2012 at 8:13
  • An important piece of advice that's missing in the answers is that FTL is a game that you have to be playing for the final boss. From sector one, you have to take into account that you'll have to be fighting that guy, and consider how your choices in weapons and augments are helping you with it.
    – Jack M
    Apr 20, 2014 at 20:40
  • 1
    @JackM: it doesn't have to be that strict though, early on economic augmentations may pay off more than offensive/defensive augmentations, but they'll be useless on the boss, so you'll want to sell them and replace with other augmentations in the penultimate sector.
    – Lie Ryan
    May 4, 2014 at 15:29

17 Answers 17


I have beaten him 5 or 6 times now, all on easy. General strategy is:

  1. 4 points in shields, duh.

  2. a dodge around 40%. This takes 4 power to engines and having both the engine crew and pilot crew be maxed out in their skills (actually, that's about 37-39% I think?).

  3. Some good, old fashioned luck.

  4. Plenty of spare crew. You'll need the usual party of Rogers and Hammerstien men to run around and punch intruders and also provide back up repairing. Don't underestimate that last part. Racing to get systems back to health ASAP can really help.

There's nothing fancy about how you attack. You throw every single thing you have at him, try to overwhelm the shields, and then do damage. My preferred strategy is beam heavy, but I will use launchers depending on what I find along the way. Since he's got excellent dodge and 4 shields, you've got to alpha strike every time you hit him (that is, fire everything or nearly everything). Once you damage his shields enough that you can get to critical systems easily, you still need to periodically attack the shields because they'll get repaired.

Another good trick I learned is do not fire your weapons as soon as it comes up. Wait till you can fire all your weapons at once for the first barrage. This will help overwhelm the shields helping you bring them down and damage them. Once the shields are down feel free to fire at will.

Now, ideally I would have something like Blaster mark III (5 shots, 1 damage each, 4 power), blaster mark 2 (3x1, 2 power) and maybe a heavy laser (2x2, 2 power). Or a small bomb launcher (underrated, it does 2 system damage). But really any number of things can work. I think I just beat him with the Kestrel using a Blaster Mk II, Heavy Laser, Halberd Beam, and Small Bomb Launcher. Obviously a crew member with maxed weapons skill is really important. Barring an accident, you should have that no problem. If you have less than 6 points of active weapons, you are probably going to have a rougher time of it. I prefer to have 7 or 8.

I will say this, I believe I have observed that e.g. the Heavy Laster (shoots twice, 2 damage each) will only eat 2 shield points up if it hits both times. I always like to have a blaster in my arsenal, but fate won't always help there.

There are two augments that, other things equal, really help in this fight:

  1. The "decrease weapon recharge time" augment. Nuff said. This is always the augment I hope to get first unless I'm going early cloaking.

  2. The "when you warp in all weapons are charged". You might think this one won't matter as much but do not under-estimate it. It's a free volley to open the fight!

With the first augment and a great gunner you'll be attacking every 13-14s at most I think. From there, it's back to luck. If he rolls exceptionally well on dodges (and you don't), it can go south and there's nothing you can do about it. I've lost to him with a number of promising ships for this reason. Tip your cap and go have a drink.

Cloaking is really powerful for ships who can get it, e.g. the kestrel. My poor federation cruiser is no longer cloaking eligible, but I have beaten the last guy several times with cloaking + cloak weapons. For form 1, the weapon on the inner-right side of the boss ship (actually, this one is always there but see below) is a freaking Gatling missile launcher. It shoots 3 missiles and it's super scary. I prefer to cloak when this is fired (and hopefully he'll be shooting other stuff too). Ditto for form 2. Form 3 will be something you have to discover on your own. Obviously if you run cloaking stealth weapons is a huge priority. But the 100% dodge you get from cloaking is really useful in the fight, so not having stealth weapons is not the end of the world. If I have cloaking I always try to get it to 3 points, but I consider 2 the minimum. That can buy you a lot of time to repair systems or deal with borders.

Doors 3 is really useful starting on form 2 of this fight (and really useful in the last few sectors!). I usually save that upgrade for late though.

Andrzej Doyle is absolutely right that boarders can be really useful in this fight. It's important to keep in mind that there is no one path to victory. After the beta update that took away cloaking Fed cruisers, I managed a few more wins. Mostly beam-heavy stuff but I made great use of bombs in two cases (I love small bombs because they only eat up 1 power but do 2 damage). I had a mixed-arms game (using some boarders) go really well until I ran out of places to repair and then lost in the second form.

Targeting priorities: Shields are first priority, obviously.

  • Form 1 I like to go after the Gatling launcher next. Then it depends. Weapons or engines.
  • Form 2 I go for the drone bay before the Gatling launcher usually. The ship will throw a lot of drones at you. This helps alleviate that.
  • Form 3 Back to targeting weapons.

Lastly, it takes more luck. Sometimes you'll prepare to do this series of fights and have repair nodes/stores near by that you can use to stay fresh. Sometimes you won't. I have lost promising ships that way too - a node got swallowed while fighting the first or second form and I was too beat up to finish him. Them's the breaks.

It took me a number of tries to beat him, and it can get frustrating. Stick with it. You'll break through eventually.

  • I should note I have beaten him lots more since I wrote this. However, not once since the game was released :)
    – peacedog
    Sep 17, 2012 at 19:26
  • Good advice. Beat it on Normal last night, and if anything, the boss fight seems easier than it used to (though I find it harder to get there in the first place). The key for me was a teleporter to take out their weapon systems (particularly missiles!), having ~40% dodge, and 4 shields. Weapons were less important... I did it with a single hull missile launcher (with ~50 missiles) and a Burst Laser 3 (which spent the entire fight disabled, except for dropping super shields in phase 3). That said, it got pretty tense in phase 2, since I didn't have a reliable way of keeping their drones down.
    – Sterno
    Sep 17, 2012 at 19:36
  • Nothing but anecdotes here - I didn't pay that that much attention to the updates during beta - but I think the final boss use to dodge more. And that there is less scrap available getting to him ( to the tunes of hundreds of scrap by the Last Stand). I would agree he's easier now but harder to get to.
    – peacedog
    Sep 17, 2012 at 19:55
  • 2
    If I remember correctly, you can pause at any time if you feel overwhelmed, assign some tasks, and then continue.
    – nevets1219
    May 8, 2013 at 22:36
  • 1
    This answer is dated; I'm going to revisit it in the next few days.
    – peacedog
    Apr 8, 2014 at 19:36

In addition to peacedog's excellent write-up above, I find boarding parties can make things much easier. Each of the boss' weapon systems is in a standalone room, manned by a single human - which means two of anything should be able to beat him in combat, then destroy the weapon.

It does reduce the crew you have available for repairs and boarder-repelling, but it's also a "free" destruction of a weapons system every 45-60 seconds or so. This can make the incoming damage much easier to take, especially if you take out the most troublesome system first (Gatling missiles, I would say!). If you have a full complement, it shouldn't be too hard to keep things under control with 6 people back on your ship.

(Or of course, a single Mantis, Rock, or combat-trained human/slug should be able to take the gunner out, so in reality you could manage this with seven back on your own ship - if you don't mind the destruction of the weapon taking a few seconds longer.)

  • 19
    NOTE: Leave at least one enemy alive on the ship; if you kill all its crew the AI takes over and it can repair all systems simultaneously. Feb 16, 2013 at 11:23
  • 5
    As for which enemy to leave alive, I recommend the guy who mans the laser, second from the left at the top. Why? You want to kill the crew in the main rooms so you can use boarders to destroy cloaking, shields, and drones. The crew manning the ion and beam weapons on the left and right will automatically die after the first and second phases, so you can’t count on them staying. And the third crewmember from the left mans the missiles, which are a much greater threat than the lasers. May 18, 2013 at 22:35
  • 1
    Alas, in the Advanced Edition, the laser and missile rooms are now connected to the rest of the ship, which makes taking out its weapons with boarders a lot harder than it used to be. (Or so I assume; I didn't even try.)
    – Kyralessa
    Apr 7, 2014 at 2:09
  • 1
    @kyralessa Are you sure that's true? I beat the boss last night (with Advanced Mode content turned on), and the layout seemed to be the same as ever. The boss has hacking drones and mind control now, but the laser and missile rooms were still standalone for me... Apr 9, 2014 at 7:26
  • 4
    @AndrzejDoyle: The weapons room is only connected on Hard mode, according to ftl.wikia.com/wiki/…
    – Lie Ryan
    May 4, 2014 at 15:41

What makes a good boss? A boss fight should be representative of the rest of the game, only harder. The FTL boss is a great boss fight. So like the rest of the game, there are many strategies.

However, I think boarding gives us a real edge over the flagship. I've yet to beat the boss with firepower alone.


Each of the flagship's four weapon bays are isolated, making them easy targets for teleporter away teams. I like to destroy the missile launcher first.

Killing the crew in the main section of the ship is much harder because of their number and the deluxe medbay. Still, if you have the opportunity (while the flagship's weapons are disabled) it's worthwhile to decimate the rebel crew to put them at a disadvantage in the next engagement.

Caveat lector: Do not exterminate the flagship crew, else the dangerously competent AI takes control, quickly repairing the ship.


Cloaking is really useful to evade the flagship's "power surge" attacks. A 1 power cloak is sufficient—if you're smart you can cloak in sync with the power surges.


The flagship's triple missiles are deadly. I've found that two defence mark I drones protect better than a single mark II drone, because the mark II drones are distracted by lasers, sometimes letting missiles pass.


The boss is much tougher than the rest of the game. If you limped through the penultimate sector with a skeleton crew, you're already finished. You need to arrive at the admiralty with a 30 power, 8 crew, star destroyer. How to do that is a question for another post. You'll need to collect a lot of scrap.

Edit: Beat the boss on normal for the first time! This was in the Mantis ship with the size 4 teleporter bay. I used the strategies above.

  • 2
    The AI also repairs /all/ of the systems simultaneously -- even the weapons systems that the regular crew can't get at. Oct 10, 2012 at 15:19
  • That answers my question whether eliminating the crew would skip the other to encounters...
    – Zommuter
    Jan 13, 2013 at 19:34
  • 2
    Killing the crew isn't such a big problem, it means your boarding party have free-range on the ship to keep all the systems down and do 1 hull damage each time they are repaired. Just don't kill the O2 unit!
    – Nick
    Feb 19, 2013 at 17:34

My usual boss-killing build tends to be roughly this:


  • five points in Dodge (that's the tipping point to diminishing returns)
  • at least three bubbles of shields, preferably four if you had the cash.
  • a Cloaking Device (with one point of energy - upgrade if you got the cash)
  • Transporter with two or three levels (two is kinda minimum)
  • all the crew you can find (preferably a couple combat guys, but that's just gravy)
  • upgraded subsystems (particularly doors!)
  • enough weapons/drones to punch through for 5+ damage. (The boss has four bubbles of shields, so you need to get through that.) Obviously the specific weapons depend on what the RNG gods bestow.

Overarching Rule

For every other fight in the game, you auto-win if you kill all the crew. That isn't true here. If you kill the entire crew, a robotic AI takes over and the fight gets harder. So you need to keep one guy alive - usually it's the guy manning the lasers since he's trapped and rather ineffective once you take out the other weapons.

Tactics - stage one

  1. ASAP: get two guys over to the missile launcher (third weapon from the left). That's the scary gun, and it needs to go away ASAP. Once that's dead, beam back, heal during the transporter recharge, then get over to the other weapons (I usually hit the beam on the far right next, then the ion on the far left). Remember to leave the lasers alone (that's the second weapon from the left)
  2. Meanwhile, watch for the missiles to launch. When they do, cloak. You really don't want to get tagged by those.
  3. All other weapons start punching down shields. Once you're getting through, you can target other systems or whatever works best with your weapon loadout.
  4. Stage one boss has it's own cloak (and a disgustingly high dodge), but other than letting the shields recharge and getting in some healing, it's not that bad. Try to make sure your boarders are on the ship when it cloaks - they'll keep the beats going.
  5. Once you've cleared the weapons, it's time to clear out the rest of the crew. I usually try to beat the shields down a couple points, then switch to the medbay. Once you've got it destroyed, beam the boarders to that room, start picking off crew. (Obviously, if you've got fire weapons or anti-personnel drones, keep that fun coming as well!). The goal is to kill all the crew (excepting Mr. Laser) before you destroy the ship.

Once you beat down the ship, the left chunk (holding the ions and blessedly the shields) will break away, and it'll jump. (Do make sure your guys weren't on the boat at that point - you'll lose them!). Make your repairs, heal up your boarders, and follow to encounter...

Boss - stage 2

The bad news is that it's completely repaired (excepting the lost chunk) and it's realized it has drones (and lots of 'em!). The good news is that the crew doesn't regenerate, so all that's on board is Mr. Laser.

  1. Again, get the boarders over to the missile launcher and take it out ASAP. Then the beam. Then, start taking out main systems (shields first to bring your weapons into play). Again, remember to get off the boat before it blows up.
  2. You'll probably need to cloak for the first missile salvo, but after that what you're watching for is the big red WARNING message. Don't cloak yet!. Wait for the moment when you see the big swarm of drones, pause, then cloak. You only want one point of energy in cloak here - it's enough to cover the swarm (which will beat the holy hell out of you), but the shortened cloak means you'll have just recharged in time for the next assault. (Unfortunately, taking out the drone control system doesn't stop the swarms).

The wiki says this is the hardest stage, but I've never personally had a problem with it. YMMV. Once you've destroyed it, it'll lose the right side and jump away. Heal and repair, and if you have spare blocks, divert power from transporters (but leave the guys in the bay) as you follow and encounter...

Boss - stage three

This version only has the missile launcher and the laser, but it'll send boarders all over the place. (Luckily, you pre-killed the crew, so you only have the odd boarding drone to deal with.) On the downside it starts with one of those Zoltan shields, so you can't board at the start. This version does a beam-spam attack (again, you'll get the WARNING before it fires).

  1. Knock the Zoltan shield down ASAP. Preferably you'd like to knock the missile launcher out of commission before the beam spam starts.
  2. The moment the Zoltan shield is down, push power back to the transporters and take out the missile launcher. After that, your targets are shields and drone control - the boarding drones will continually spawn until that system is destroyed.
  3. The beam spam is remarkably slow - you can wait until you see the ship fire before pausing and cloaking. Early on, if you have to choose between dodging the missiles or the beams, dodge the missiles - I find they have a lot more punch. (The beams will probably damage a bunch of systems a little, but not enough to get you in real trouble).
  4. The boarding drones can be troublesome depending on where they land. If you've got triple-strength doors, you can let them bang away for a while in empty rooms. Otherwise you'll have to detail some bodies to take them out (and fix the breaches). Again, depending on what crew you got, you may need to pull your boarders back to help out. On the plus side, you can pull your weapons and shields guys to help out.
  5. Every so often, instead of beam spam the Zoltan shield will recharge. But since you should have knocked out the weapons by that point it's more an annoyance than anything else. Just shoot them down again and continue.

Again, make sure your guys are off the ship before it explodes (unless you're in the mood for heroic sacrifices), and you're a winner!


  • With a four-bay teleporter with a fast recharge, you can get remarkably far without heavy weapons at all - just send the initial groups over in twos to take out the weapons, and then send them four-at-a-time to do beatdowns. (You need that fast recharge though to make sure everyone stays alive).
  • Alternatively, if you lucked out and got some good guns (say, a couple ions or a mess of Burst Lasers), you can skip the boarding entirely and just boom through the shields. Some Defense drones can take the sting out of the missiles, for instance.
  • great post, this is pretty much the same way I approach the final boss. Boarding really does make the fight so much easier as long as you know the trick of leaving 1 alive. I'd +1 you but I'm out of vote for today though.
    – l I
    May 28, 2013 at 17:18
  • Aside: Thanks to Theodore for catching my handed-ness error. May 28, 2013 at 19:27

To supplement other answers: If you can get one, running a Defense drone -- even a simple Mark 1 will do -- will give you a significant edge:

  1. It will stop some incoming missiles. (Taking out the enemy ship's capability of firing missiles at you should be a top priority, but the defense drone will help until you can get that accomplished.)
  2. It will destroy (most) incoming Boarding drones before they can breach your hull and board your ship. (This is a very useful "undocumented feature" of the Defense drone!)

If you really want to do the fight with weapons only, I recommend a hull laser and two Burst Laser Mk.III's. Go for the drone control first because the drones have been my bane on that fight many times.Then autofire at least one on the teleporter.Then you have two options; either focus on the weapons of the shields.I usually go for the shields.


It's easier than it seems. Just disable its shields as fast as you can (having ion bombs helps here), then go for his weapons: If you have a lot of evasion, disable his lasers first. Or, if you have maxed shields then disable his missiles first.

To disable the weapons, send a boarding team to one and attack another while you keep a weapon at the shields so they don't come up. Once it has a couple weapons disabled he shouldn't pose much risk and have just a few life left.

  • 3
    Always go for the missiles first. Mar 13, 2014 at 18:58

I've just completed my first run on easy. No teleporter, no cloaking, no fancy stuff. 6 crew members (3 humans, 3 engi), 3 shields.

Pretty crappy ship, huh?

Luckily I had gotten two anti-ship I droids which helped bring down the shields, along with 4 weapons (Artemis, Blaster I, Blaster II and Hull Blaster I). At the end of Form 3 I was nearly dead with all the boarders and breaches popping up in my ship, but I kept on whacking the shields with everything I had and it went down at last.


Three words: Hull. Repair. Drones.

These bad boys give you 3-5 hull reparation for two points of power and a drone part. They're absolutely fantastic when your hull takes a dive mid-combat, or you need to repair out-of-combat. I've personally found them to be a bit rarer on the RNG scales, but they're absolutely amazing little buggers.

If you've got other drone schematics in your cargo hold, you might consider swapping them out when you leave combat in order to repair -- it's more or less free, instant hull repair at that point anyway.

  • 1
    So something to note with this strategy: If you have the drone recovery arm you can jump while the repair drone is working and it will be recovered. Two points of hull reparation for free after every fight.
    – Probst
    Feb 12, 2016 at 16:28

I have an enhancement to Allen Gould's tactics for the first stage to kill most of the crew. Hacking provides an opportunity to kill most of the crew without having to attack the med bay. This can be handy if you can't get through the shields reliably, and it's easier to control without accidentally blowing up the mother ship early.

Follow begin killing the crew in the weapons pods. Get a hacking drone on the shields ASAP. This will both let you begin shooting at the ship, and (this is the important bit) it locks the doors on the shield room cutting off the pilot.

Once you've knocked out the weapons, we can begin slaughtering the crew at our leisure. This takes advantage of a few predictable bits of AI crew behavior.

  1. AI crew will rush to defend other crew.
  2. AI crew will also rush to the cockpit if it's unmanned or damaged.
  3. Wounded AI crew will rush back to get healed if the medbay is online.

Be sure to leave the medbay alone, it needs to be online for this to work properly.

Teleport two soldiers into the cockpit. The AI crew will begin banging on the door. While they're doing that, kill the pilot and let them work over the cockpit.

Eventually, two AI crewman will burst into the room. Here's where the fun begins. Fight them. Once they're wounded sufficiently they will attempt to flee to the medbay. By this point, the door out will have locked itself again. The AI crew will frantically bang on the door while you shoot them in the back. You should be able to easily kill them before they can get through the door.

By now your boarding party is probably badly wounded. Teleport them back to the ship for healing.

Rinse. Repeat.

Variations on this technique include running between the cockpit and the shield room to try and isolate individual or wounded AI crew using the hacked doors. It can become a bit of a French farce.

Lantis are incredibly valuable for this technique, as asphyxiation will greatly increase the number of AI crew they can kill before having to return to the ship. Or, if you can get control of the shield room, they can asphyxiate repair crews as they bang on the cockpit door.

This technique can also be implemented with crystal crewmen or a lockdown bomb using lockdown on the cockpit.


100% Boarding Strategy-Not for use in Hard Mode


Systems required: Cloak, teleporter, clone bay (recommended) and hacking (optional)

Upgrades: Level 3-4 shields, level 2-3 teleporter, level 1 cloak (its recharge will come fast enough for power surges), level 4-5 engine (for 100%+ cloak dodge rate)

Preferred weapons: Ion burst mk II or ion bomb (with weapon pre-igniter) for zoltan shield), high-dps weapon as a finisher (beam, flak mk II, chain vulcan, etc.)

Preferred Augmentations: weapon pre-igniter, automated reloader (if you have good burst damage weapons); reverse ion field (for the boss ion, although it becomes obsolete after the first stage); reconstructive teleport, zoltan shield bypass (for boarding)

Preferred Crew: 4-5 mantis/crystal/lanius/rock (in terms of effectiveness; mantis will take out the missles, crystal can be used to prevent crew from going into the medbay after the missiles are down, and lanius and rock are simply other good boarders)

Stage 1

Important: If the boss hacks any crucial system, be prepared to jump out.

As soon as the boss comes out of its cloak, send two boarders into the triple leto launcher. Cloak yourself (any level cloak will do for this stage) when the missiles come at you. When your teleporter's CD is up, teleport into the ion blaster. Retrieve your crew from the missile launcher once it's destroyed and teleport them into the beam weapon, then teleport your crew back from both weapons when they're destroyed. Now, to destroy the rest of the ship's crew (leave the triple laser man alive, or else you will face the wrath of the AI!) Do not fire any hull-damaging weapons as you don't want to leave your crew on the flagship as it jumps away!

-With Hacking

Teleport your crew into the medbay. When the ship's men come to fight, send your hacking drone at the medbay and hack it. This ensures that the enemy crew will have a tough time trying to escape your crew and will not fight them in the process, saving your crew from damage.

An alternate hacking strategy is to hack the doors subsystem and activate the hack when enemy crew is at low hp and you don't want them to escape.

-Without Hacking

Some ships can only hold 2 additional systems, or your luck at shops has run out. Although this can make things difficult, killing the crew in the main part of the ship is still possible.

One method is to destroy the medbay with weapons (make sure you don't reduce the hull to 0 doing so), then teleporting into the medbay as to prevent the enemy crew from repairing it. Clone bay is helpful here as you will be dealing with 2 v 4 situations while trying to teleport additional forces in.

The other method is to send 4 mantis into the shield room (in 2 waves of 2 or all at once using the crystal/mantis ship). If done correctly, only one enemy crewmember will enter the room at a time and will not be able to escape as the mantis's DPS is too high.

-Both Methods

After the enemy crew has been killed (with the exclusion of the triple laser gunner), give them the gift of free XP by destroying the ship's systems (excluding oxygen and the triple laser weapon). Keep in mind that destroying a system will deal 1 hull damage. Then, use whatever weapons you wish (basic laser, mini beam, etc) to destroy the helpless 0-evasion ship. I sound like a broken record, but don't kill the triple laser guy!

Stage 2 Now that the enemy has no crew in its main section, your crew can destroy systems uncontested. Your first boarding move should be into their drones system or missile weapon. The first point of damage to the drone system will disable their boarding drone. Cloak (lv 1) whenever the triple laser is firing with the drone surge; lvl 3-4 shields should hold up the power surge by itself (unless the boss beam is still up). Destroy shields and piloting only if you're desperate to destroy this stage; if not, you can destroy all the other systems (except oxygen and the triple laser). Again, use whatever you want to get rid of the hull when you feel like you're done.

Stage 3

Cloak every power surge except the regen zoltan shield ones.

-With zoltan shield bypass:

Board aggressively, trying to disable the missile launcher and the mind control. Deal whatever dps you can and try to beat the boss! Tip: you can leave crew on board the flagship at the stage; it's the last fight anyway!

-Withough zoltan shield bypass:

Use ion weapons if you have them (they deal double damage to zoltan shields). any salvo weapon is useful as you will want to get rid of the shield ASAP. Teleport into whatever you want (except the two aforementioned systems) and try to deal whatever damage you can.

Why is cloaking essential to this strategy?

Crew takes a much longer time to damage systems than weapons, and you will have to wait for extended periods of time waiting it out.

Congratulations! You have beaten the rebel flagship!


If you can get 2 Ion Cannons with a Blast Gun using a 1 power, and have 2 droids, 1 for blasting incoming missles, and 1 for attacking. Around level 6-7 get the repair droid. Don't bother with shields 4, 3 is enough, make sure to focus on getting guns first, people second, and subsystems last. If you have droids, the automated thing that gets your parts back is a must have. Anyhow, have fun! Engines I didn't even get up that much, one less system to worry about. I'd rather cloak.


Having a full strength cloak and hacking tool definitely helps. Also simple things like lining up your weapons fire to ensure a few shots get through the shields.

By the time you get to the final sector you should have a full yellow skilled gunner. This generally means that unless you have VERY slow weapons you'll be able to fire before the mothership.

With this in mind I usually keep the first cloak until after I've fired. I fire, he fires, the moment the first missle leaves the launcher, pause and cloak (removing weapon targets as you do so they don't fire). You should at this point have been able to get a decent volley of fire off at him (probably dropping the green shield) and taken little punishment in return. If you have a boarding party send it straight at the missle launcher the moment the green shield is down. All weapons should be trained on the shield room until the shield is completely dead and the rooms is regarded as a lost cause by any remaining crew.

Had a very OP run in a slug type C cruiser last night. Entered the final sector with 4 chain burst lasers (8 synchronized shots :D :D ). With that, a hack, and a cloak, the final boss wasn't really much of a challenge.

Small point to not - while defence drones will usually kill a hacking drone the anti drone defence drone will often only delay it (sits spinning/being electrocuted but will often then carry on to target).


I actually beat it with the kestrel and 3 crew members with no teleporter. basically, i had max lvl cloak, hermes, artemis and burst laser. i spammed shield system on all 3 fights


I have been beating the boss with relative ease following the same strategy as the first I've beaten it.

The most important thing is to have good weapons, not only to damage it, but also damage the enemy critical systems, like weapons and shield. The weapons also can't be repaired if you kill the guy manning it since they are isolated from the rest of the flagship. So if you damage that weapon and kill the guy, you don't have to worry about that anymore. Useful for enemy missiles.

I try to have at least 2 lasers with 3+ shots. If I have those 6+ shots, the first half is stopped by the shields and the second half succeeds. Burst Laser Mark III fires 5 shots, which makes it perfect for this strategy.

It helps to have another weapon, like a missile or bomb that is able to kill/breach/fire.

The other systems you should focus are:

  • Engine: Increases evasion, making their attacks fail. Since they will shoot a lot, this makes it top priority. (Level 4/5+)
  • Shields: Stops many kinds of shots, like Lasers, Ions and Beams, making their attacks fail. Also top priority. (Level 6+)
  • Cloak: They can't attack you, if they can't see and lock their weapons on you. If you can, you should buy it and maximize it. If you can't, spend the scrap saved on maximizing Engine and Shields.
  • Doors: If they board you, you might be able to make them hurt, flee or even kill them by good door management. The focus should be on using paths of open doors directly to space to create vacuum, making them suffocate and lose HP. Increasing the Doors system level makes them very hard to open, giving you time to suffocate them. The harder, the more they will be exposed to the vacuum and more chances for them to being either killed or return to the flagship. This is specially important when you don't have many crewmembers or they are weak.

Camp the base so you can pay for repairs between battles. Just wait for them to come back. Your ultimate strategy will depend on your loadout. Things I use, below. TL;DR : utter brute force via en masse energy weapons; automated system repair and healing.

Lasers with a DPS equal to half their energy cost, with the fastest recharge you can find. 2 MKIIs are better than 1 MKIV. You start with one of the best weapons in the game, the Burst Laser II. You just need three more of them, or as close as you can get to those specs, until you find a Flak gun or a Vulcan cannon to augment your volleys.

Volume of fire is better than damage numbers; put all your eggs in one basket and it could miss or be shielded. The longer they take to charge, the more susceptible they are to downtime. BLIIs are the happiest medium. Strictly speaking energy wise, I don't think there is a better weapon: 2 energy for 3 damage.

Anything you have to micromanage is no good - I'm looking at you, you stupid beam weapons. As well as all aspects of your ship, the more automation the better, which is why you need these too:

System Repair Drones (yes, plural). Don't waste a spot on Fire Suppression. Between these and you opening doors, fires shouldn't be a problem.

Medibot Dispersal. There's nothing worse than losing a fully intact ship to the enemy after a bunch of beeps go off. These will also let you safely run your ship with de-oxygenated corridors and useless rooms. Fires self-extinguish and borders will be half dead.

If I don't have a good set of lasers and at least either the bots or a system drone, then I don't wonder why I lost.

Lasers get the job done, and those automated systems keep you from having to micromanage the crew between repairs, staying alive, and doing their actual jobs. If the enemy hasn't done so yet, the priority target is the teleporter. Because your job is to pick targets for your guns; you ain't got time for a second front. Anytime you stop looking at their ship and have to at yours, the battle has taken a turn for the worse.

The only thing that should be left for you to do is to deal with the borders that do make it (and send people to fix the oxygen if the drones are down). With Medibots, any crew member can handle borders, so don't waste drone parts on (... anything other than SRDs) Anti-personnel Drones, which don't heal in combat and are just a quickly destroyed expensive stopgap.

Things I don't use unless I'm bored : bombs, missiles, hacking, teleporters, mind control, cloaking, and drone ships or personnel. Things I don't put points in : piloting and engines (both rely on RNG, and I don't gamble), and sensors (are useless without the other 'toys'). I treat these battles as timed exercises. You're under artillery fire the entire time and therefore in an unsustainable position; speed is key.

The only is objective is to do more damage to them than they you.

From the beginning of the game, do not lose site of the objective, nor resort to all those other options available to you that do not directly help achieve said goal. If you've been blowing your money the whole time, and don't show up in the final system with ~200 scrap for repairs and in a ship capable of ~1 DPS, good luck.

Essential systems, like Oxygen and Medbay should be upgraded at least an extra point so as to have a damage buffer. Beyond that, oxygen is a critical system, and should be 'maned' by someone who's good at repair if you've got extra crew.

IME of save scumming these fights, the degree to which RNG plays a part is appalling. It can go either way in about thirty seconds. Absolutely every ship in the game is a glass cannon, and there's only one way to win if you're a GC... Keep 'em firing!


Everyone hates the Rebel Flagship, mostly because it eats you super early. I have found many ways to defeat it, have tried them, and almost won, yet I just didn't have the luck. Here are some lists, first for the essentials to win, then the if luck goes your way, and lastly, the highly recommended. You may think that these are horrible categories, but trust me, you'll see why. I have defeated the flagship once using kestrel (and everything on this list) and my hull bar didn't even turn yellow!


  • Level 5+ engines
  • Level 3+ Shields
  • 1 crew to man every station
  • A Burst Laser (minimum Mark II)
  • An ion weapon
  • A spare mantis and human pair (to deal with boarders)
  • Small Bomb


  • Zoltan Homeworlds (To get the quest for the super shields)
  • A few Zoltans
  • As many free crewmembers as you can get (fight slavers and have surrender)
  • A Burst Laser Mark III


  • Crew teleporter
  • Any type of bomb
  • Fire weapons (If you have ability to wreck shields)
  • Drone Control
  • Hull Repair drone
  • Loads of explosives AND drone parts
  • Cloaking 2+
  • Level 3+ doors

These things will all help, especially since the new update where (on easy) the flagship has only 3 shield barriers.

The Strategy

PHASE 1 The first thing that happens, the flagship will cloak. Don't plan where to fire weapons. just pause during the whole "you prepare to fight the flagship" and plan a teleport (if you got it) of a pair of humans into the missiles (because everyone hates them) and do nothing except cloak (if you can; when the missiles just fire) and dodge. When the flagship becomes visible, your boarding crew will kill the enemy in the room and start to break missiles. Once done, beam back, send to heal station, and follow through with this weapons plan once. Fire ion. The moment the ion make contact with shields, whop the shields if you can get through. Otherwise, launch small bomb on shields same time as ion, and once the ion lands (after the bomb, ions are slow) fire all you've got, especially fire bombs. Then repeat boarding technique on enemy ion weapon, and once they beam back, fire weapons plan once more. Next, repeat process on beam system and fire more volleys, but DON'T do same for regular laser. Leave the guy in there and repeat weapons process once every weapon is charged until ion weapon and cloaking break apart.

PHASE 2 Flagship will NOT cloak. People will not be in weapons rooms, just the laser room. If you beam your crew aboard and they start breaking stuff, you will eventually see something near the jump button saying "Power Surge Detected". A bunch of drones will appear and start wrecking your ship. WARNING! They are NOT controlled by the drone control. Also, you won't have much time to do the boarding process, as the enemy will have a boarding drone. If you have one, leave an engi outside the room, and put your best fighting crew inside. Once the boarding drone is dealt with, have your boarding party on your ship and DESTROY THEIR DRONES SYSTEM! When that is down, fire a volley on the beam artillery. Then repeat process on drones till flagship breaks apart.

PHASE 3 Take down their 10-point super shields and beam aboard the missiles. you will again see the "Power Surge Detected", but this time it isn't drones (that broke apart last battle). it will fire 9-12 heavy lasers than can eat you. Either the 2nd or 3rd "Power Surge" will cause the super shield to restore. You need to be careful of that, as your crew can get locked aboard the enemy ship. Once all is said and done, you should get your crew back on your ship and target their med-bay. Once you have done something significant, like a breach, they will try and fix it. Keep firing at it until noone will enter the room. Once that has happened, try to kill off their crew (except the guy/gal manning the lasers) with your small bomb. Once their crew is dead, fell free to destroy whatever you want (and maybe ion their weapons, so as not to hurt the guy in there). As soon as the flagship is near destruction, kill the last guy, it'll be funny. Then destroy it.


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