FTL has got to be one of my favourite games of all time, it's balanced but challenging game play is fun for hundreds of hours. However when starting off it can be extremely difficult and frustrating to win against the flag ship, this is my guide for how to do just that.

Each run is different, with different ships and different encounters through the 8 sectors, This guide isn't always always going to work, getting through the sectors is your job, this guide is mainly focused on how to prep and what to do once you make it to the final battle.

It's worth noting there are many ways to beat the flagship with different augmentations, weapons systems and strategy's all with varying levels of success, this is the way I discovered first but found success with different variations the better I got at the game.
Thought I would share with someone who is struggling to get a break :)

Big guide and lots of words incoming

It doesn't matter what ship you use as the concept is still the same, however some ships have an advantage over others because they already have some systems you need installed. Personally I love the stealth cruisers.
There a few things you are going to need to collect through the sectors to face this monstrosity.

Weapons:
It doesn't really matter what weapons you collect, they just need to be able to do enough damage to break through 4 layers of shields and the flagships stage 3 super shield.
The weapons you collect are entirely down to personal preference, however flak 1 and 2 weapons are great against shields so I can recommend these. otherwise it's also helpful to have a big burst laser to break through the shields.

Augmentations:
Similar to weapons, Augmentations are down to personal preference and what helped you get through the sectors, however some are more useful than others in the flagship fight.
It can be helpful to try and collect augmentations like, Slug Repair Gel, Fire suppression, Engi Med Nano bots, Super shield bypass, as these will give your crew a massive advantage in the fight.
Early game it is so helpful to collect Augmentations like Long range scanners and Scrap Recovery arm as these will help your scrap collection immensely.

Systems:
This is where we start getting a little more complicated, the 3 Systems you need are:
- Stealth (Level 2 or 3 ideally)
- Mind control (Any Level)
- Crew teleporter (Any Level)
Engines: As you will go through the sectors you should make sure to upgrade your engines to at least level 4, this will add extra evasion onto your ship and make your life a lot easier when the Flagship used it's power surges.
Sub-systems: Upgrade things like Sensors to at least level 2, doors to the maximum and a couple into Piloting.
Med/Clone Bay: I like to upgrade my Medbay to at least level 2 as you will be using it a lot during the fight.
If you are using the clone bay, fully upgrade it.
Sheilds: Make sure to have your shields to at least 3 shields, although 4 is preferred.
Any other upgrade are up to you, however I recommend having these upgrades. Get the maximum power you can out of your reactor, you will need it.

Crew:
Through your travels you will need to collect as many crew as you can, level them up as much as possible as this will help tremendously. Make sure to always have at least 1 crew available for the teleporter at all times. I like to have 2, usually a Mantis and a Rock.

If you've followed my advise up until this point, with a bit of luck you should have a pretty bad ass ship. It's time to take on this monstrosity.
Strats
The first stage is all about killing the crew, once the crew are all dead, the ships AI takes over, but more importantly repairs at an incredible slow rate, this is what we take advantage of.

(EDIT). With a bit more playtime and a few people mentioning, it can be better to leave 1 guy alive as to stop the slow auto repair AI. This is a totally valid strategy as well, A little easier to manage too. You will have to either keep an eye on the guy trying to fix things, keeping him alive, or keep an eye on the slow auto repair of the ship. Whichever you prefer


The Flagship will jump into stealth straight away, but save your stealth for when the flagship shoots its triple missiles at you, these will devastate your ship depending where they land.
The flagship will also shoot its hacking at you, depending on where it lands, it will either be a massive pain in the ass, or no problem at all, in the end it shouldn't matter as you can just work around it by either shooting at the room or timing your systems well so it has little effect.
Once the flagship is un-stealth'ed, your first step is to teleport your crew into the small weapons room containing the triple missile launcher, this is the most dangerous weapon on the ship.
This room is marked (1) on the picture
Your crew should kill the enemy crew and destroy the missile launcher meaning no more missiles, Nice.

Re-call your crew and get them into the Med bay for another attack.

Once healed, get them back into the teleporter and teleport into the big beam weapon weapon room marked (2).
This laser can start fires on your ship that your crew can't realistically deal with while fighting the flagship.

Once that room is destroyed, recall your troops, get them in the med bay and do the same for rooms (3) and (4), the triple blaster and triple Ion respectively.

Now you have just disabled all 4 weapons and killed 4 crew, nice, now the Flagship cant deal damage to you. (If the flagship repair any of its weapons room, teleport your crew in there again and destroy it).
But we still have all the rest of the crew to deal with and if you teleport your crew in the main area's, the enemy crew will just kill them.
To get around this, get your crew to stand outside your teleporter and mind control an enemy crew mate from the flagship, then use your teleporter to re-call the enemy mind controlled crew from the flagship, essentially abducting him. Once the mind control wears off get your crew to kill the intruder and get them in the med bay to do it all over again. Continue to do this until all the enemy crew are dead.
(When recalling mind controlled enemies, they will usually go to your ships o2 supply room, not sure why, It can be helpful to trap them in the room with no 02 depending on your ships layout, this way you can send your crew in to break some stuff at the same time)

Once all the enemy crew are dead, the AI should take over and you will get a notice, that was the hard part, relatively smooth sailing from here on in.

If your weapons are powerful enough, punch a hole through the flagships shields and start doing damage to the hull, and it's a lot easier this time because no one is going to repair it ^_^
If your weapons aren't that powerful, teleport your crew in to destroy the shields from the inside, teleport them out and then destroy it with your guns..

Easy as, first stage down.

See stage 1.

Stage 2, here we go.

The flagship has re-routed most of its power to its now suddenly massive drone supply, wizard.


In this stage the flagship will have massive surges of power that re-animated all it's drones, you want to save your stealth for the surges to avoid all the damage the drones can do.

Similar to stage 1, we want to take out that missile launcher first, teleport your crew in and destroy that weapons room (1), It should be a lot easier this time because there are no crew to stop your invasion.
If you weapons are powerful enough, fire on the drone control room to disable all the drones, if not, recall your crew from the missile room when it's destroyed and get them into the drone room quickly.

The next step is to take out that big beam weapon again (3)
Recall your troops and take out the laser room. (4)

You have now rendered the flagship attack less again (apart from the power surges that you should be saving your stealth for).

Either fire upon the ship to destroy the hull or have your crew destroy the shields first, then destroy it again.

Make sure to not kill your crew, obviously.

One more stage to go.

Stage 3

Stage 3 is similar to the first two stages as it will involved sending your crew in again but this time is has a few more things to watch out for.

Mind control: Now the flagship has mind control, it will use this against your crew and can be a pain, just mind control them straight back, no problemo.
Supershield: This is why you need enough power in your weapons to break through this super shield quickly to get your troops in there to disable its weapons, alternatively have a super shield bypass Augmentation.
Power surges: The flagship will have even more frequent power surges, thees will either be a massive attack or generating a new super shield.
You need to save your stealth for these surge attacks, but have your engines upgraded enough so if you get caught with your stealth on cool down, enough of the shots will miss to not do too much damage.
The new shields are really just annoying, but you should have enough firepower to deal with this. (Flak weapons are great for tearing down shields)

Normally we would need to worry about the enemy crew teleporter, but all the crew are still dead so this isn't an issue.

First step is to send you crew in to disable the missiles again (1)
Next recall them and take out the laser weapon (2)
Once those are both down, the only way it will be able to attack you is with its power surges, but don't get too confident, these can do a lot of damage.

The next stage is getting your crew to attack the shields system from within and pumping as much damage straight into the hull of this thing, once it's destroyed you win the game.



Simple as that

It depends what ship you choose to play through with but they all have their own pro's and cons.
The best ships to do this with have either Stealth, Mind Control or Crew teleporter already installed.

Pausing Pausing and micromanaging will be your best friend as any seasoned FTL player will know, Especially when it comes to crew teleportation and mind control.

Disabling: If you use your crew teleporter to kill all the crew and disable ships through the sectors you get a much higher scrap reward and lots of fuel.

Bombs Bombs can be very useful weapons as they can't be shot down by drones and bypass all shields, this can be useful for taking down rooms against the flagship without having to send your crew in, just make sure there are no enemy crew to repair it.

Backup Battery A backup battery can be very useful to provide a little bit of extra power when you really need it, The best case use for backup battery is to use it's short burst of power when you need to use a system with a long cooldown (ie. Stealth). Battery's power gives out while the system is cooling down and doesn't consume any extra power on it's cooldown, with the right timing, its essentially a free system and you can devote your regular power for a better use, like Engines.

It will help to pick up Augmentations like Scrap recovery arm, and Long range scanners early on as you want to collect as much scrap as possible to upgrade your ship.

Generally speaking, the blue option is the one to go with.

Each race has their own advantage and disadvantages, its good to have a mix for blue options and versatility.
Humans: Don't do much, they learn skills slightly faster
Engi: Use for repairing, bad at fighting, useful to keep in the sensors or doors subsystem so they can leave and repair things, I like to keep an Engi hanging around in the medbay for mid fight repairs.
Mantis: Good at fighting, bad at repairing, should be used for your teleporter.
Rock: Slow, lots of health, immune to fire. Should be used for your boarding parties to soak up damage and used on your ship to fight fires
Zoltan: Used to boost power to a system, good in rooms like weapons, shields and cloaking, shouldn't be used for fighting as they are too useful for extra power.
Slug: Useful to have for the lifeforms scanner function, cannot be mind controlled, I like to keep them working in sensors.
Lanius Will strip the air out of rooms by being in it, need to be kept separate from the rest of the team, doesn't need oxygen, good for boarding parties if their are 2 of them.
Crystal Pretty late game advanced race, Best for boarding parties as they can lock rooms down with their abilities, plenty of health

Alien spiders I know it's funny, but don't do it, ALIEN SPIDERS ARE NOT A JOKE




I hope this guide helps some people out and they can have as much fun as I have had with this game.
If I can think of more tips and tricks I'll just continue to add them and I'm happy to answer any questions anyone may have :)

Also I am not a wizard, you will just have to excuse my poor punctuation and spelling, bite me.

If no one reads this guide then I guess that sucks but it's 3am and I shouldn't have spent the last few hours playing FTL and making this, yikes.

Thanks for reading.
Peace