Strategy Tips, Walkthru, and Spoilers for FTL’s Final Boss Battle

FTLGame 2012-09-16 13-53-57-07Imagine my surprise when I (Finally!) blundered my way through to the end of Subset Games new “spaceship simulation real-time roguelike-alike”, FTL, while gathering some extra screenshots for our review. In light of the random nature, difficulty, and potential for unexpected, fiery, and very permanent death, I figured I would post some screenshots and strategy tips gleaned from my fortuitous victory. I don’t claim to have a foolproof solution, or even much experience, as this was only the second time I had even seen the Rebel Flagship, but forewarned is forearmed. Especially when one bad choice can send you back to square one.

SPOILER ALERT: The following post contains screenshots and detailed information from the endgame of FTL. Those wishing to savor every surprise for themselves should stop reading and go play it themselves now.

Without further ado…

All observation and conclusions are based on FTL’s Normal difficulty level. We’re not going to cover every basic tip for combat. If you made it this far, you’ve got the hang of things.

Before Entering Sector 8: The only thing you can count on upon entering the final sector of the game is a free 10 point hull heal. There are a couple of Federation supply posts that will yield a small amount of fuel, missiles, and drones, along with an additional hull repair, but you shouldn’t count on them being easily accessible due to the random map. Go in as close to fully stocked as possible.

Recommended Gear: There are a few upgrades that I would consider essential for surviving FTL’s endgame. Tier 3 shields are a bare minimum. Additionally, I couldn’t see surviving without a Defense Drone II for its ability to shoot down both missiles and lasers. A Hull Repair Drone may suffice if you have enough drone parts.

I’d suggest having a transporter installed (for reasons we’ll examine later) and at least six crew members. A full crew of eight is highly recommended. Update: Or a fire bomb.

Finally, you’ll want as many extra engine slots you can afford for the evasion bonus. Trying to soak the amount of ordinance being thrown at you may prove impossible. Experienced crew members manning both the helm and engines with a tier 5 engine will net you a 45% evade chance. Priceless!

An advanced FTL Drive augment would also be helpful for resupply runs battles, but not necessary.

Getting Across Sector 8: Avoid combat whenever possible. It is far too late to consider gathering loot for upgrades (unless you have no other choice). Worse, you’re on the clock now. Avoid Rebel occupied systems whenever possible, ignore all pleas for help, and run from any combat you can’t avoid. Try to avoid using consumables (missiles) unless it will save you hull points (defense drones). Your goal is the flagship. Nothing else matters. Don’t be afraid to waste a turn letting the Flagship move closer if it means you won’t have to waste supplies on an unnecessary battle.

Unless you are in dire need, skip the Federation supply depots. You may need them after one of the boss fights. Just prey the Rebels don’t take them out in the meantime.

The Rebel Flagship Boss: 

And here it is! Get used to it, you’ve gotta go up against this flying fortress THREE TIMES. In spite of its intimidating appearance, this first stage of the boss does not fight that differently from the top tier warships you’ve may have been fighting. Except for the cloak. And the ability to fire while cloaked. And the four separate weapon subsystems. Okay, so it’s like nothing you’ve fought before.

FTLGame 2012-09-17 16-50-53-05

Fans of using Ion weaponry to knock out weapons are in for a shock. While you can still pin down one gun, the others will happily keep shooting you in the face. Looking at the floor plan of the Flagship does reveal one weakness: Every weapon system is in a completely isolated room with no connection to the rest of the ship. This is why I recommended a transporter. The first time the Flagship decloaks, beam two crew into a weapon chamber. I’d recommend hitting the missile launcher (third from left) first. Boarding drones may also work, but the high energy use and random landing position didn’t work as well for me. A fire bomb may be a cheaper solution, but I haven’t tried it yet.

Update: I’ve tried it now, and, oh man, is it ever a great tactic! Just fire bomb those weapon compartments. You may have to hit 'em twice on the stage 1 ship, but the gunner crew will still be dead on stages 2 and 3 leading to easy, one shot disarms.

As for the ship itself, the stock tactic of missiles to the shield generator and rapid-fire laser for other systems works as usual. Knock out the bridge to deny the enemy its evade bonus if you’re having trouble hitting. Defense should always be your top priority. There’s still a long way to go.

FTL Boss Flagship 1st Stage

The Rebel Flagship Boss, Stage 2:

You’ve gained a few extra turns to resupply if needed. Same rules apply: Avoid conflict and conserve ammo. This is where an Advanced FTL augment comes in handy.

FLT Rebel Flagship Boss Stage 2

Now were getting into the cheap, video gamey boss battle type stuff. The Flagship is down one gun and the cloaking device, but has a new ‘super ability’ you’re sure to hate. Every so often you’ll get a warning that that a power surge has been detected. This is your cue to panic. You’ll now be swamped with a bundle of Anti-Ship and Beam Drones. Knocking out the Flagship’s drone control will not prevent this from happening. There is no option other than weathering the storm and putting out fires when this happens.

FTLGame 2012-09-17 17-08-59-93

Also expect the occasional boarding drone. Don’t be afraid to transport your boarding parties home early if they’re needed on for ship defense or firefighting.

While all of the ship’s subsystem will have been repaired since your last encounter, enemy crew killed will still be dead. This will make destroying the enemy’s weapon subsystems that much faster. If you can spare the manpower to do so.

FTLGame 2012-09-17 17-16-55-82

I personally found this phase to be the hardest battle of the game. Prioritize defense and raining missiles into the enemy hull. Remember that while knocking out the Flagship’s drone controller subsystem will not stop the special ability’s Anti-Ship Drones, it WILL stop Boarding Drones.

The Rebel Flagship Boss, Stage 3 – The Final Battle:

Just like before, you get a few turns before delving back into the fire. While in my game the free Federation supply depots has vanished, a Store had opened up on the map. If you’re low on Scrap, sell everything you won’t be using in the final rematch with the Flagship. Starting with only 20 space bucks in my pocket, I was able to gather enough Scrap to buy my way back from ONE hull point to full health by selling those extra drones, weapons, and augments I knew would make no difference in the coming battle.

FLT Rebel Flagship Boss Stage 3

Okey-dokey. Once more into the breach. The Rebel Flagship is down to two guns. Good news: No cloak; No drones. Bad News: New super power; New super shields.

The first thing to note is the addition of Super Shields to the Flagship. Similar to some late game enemies, there is now a small bar next to the enemy shield display. As long as  there is ANY green in that bar, missiles and transporters will be ineffective. Use your rapid fire weapons to knock these down ASAP and watch for their occasional revival.

FTLGame 2012-09-17 17-27-44-10

Second, expect boarding parties. That Big Bad may no longer have any drones, but this is the only phase I saw her fire up that transport and come over for tea. Be ready and beam back any of your own raiding parties for extra manpower. If you can knock out the enemy’s transporter while being boarded you’ll trap them on your ship. This will prevent their escape back to the Flasgship’s medical bay and save you another tea party later. Just make sure those Super Shields are down before wasting missiles against the transporter system.

Thirdly, much like the Phase 2 Flagship, this one has a gamey boss power. At regular intervals, the Flagship will fire a huge battery of big green laser bolts at you. As with the previous stage’s special ability, there doesn’t seem to be a way of stopping it. You will still get the warning of an energy buildup before the special goes off. As usual, prioritize defense and be ready.

FTLGame 2012-09-17 17-29-53-66

If you’ve come this far, you can take this phase 3 boss down provided you’ve got half a hull, a fist full of missiles, and a bit of luck. Don’t spare ANYTHING. There is no tomorrow this time. This is the only time you don’t have to conserve your final few missiles or drones. Keep a level head. Don’t get antsy or sloppy. Good luck!

For more on FTL, be sure to check our special ‘story-style’ review and our general FTL strategy guide.

FLT victory win normal

Update: I managed to capture video of the final boss battle from another playthrough. Enjoy!


  1. Phew, finally managed to take out the flagship with a Breach Missile on easy mode... my entire ship was on fire at the time

    1. Yay! Congrats! It's a good thing they don't make you deal with the aftermath of that battle ;)

  2. Cloak lets you bypass the bullshit super attacks