FTL Game Rebel Flagship Final Boss Guide

FTL Game Rebel Flagship Final Boss Guide by GhoXen

General
If the text on the star chart isn’t clear enough, the final boss will slowly jump from beacon to beacon towards the Base. There will be a lot of free repair stations in the system, and they are reusable (i.e. use “Wait” at a repair beacon will repair you again). At the same time the rebel fleet will start claiming various beacons. You have to destroy the Flagship three times before it reaches the Base. You can repair between fights, assuming the rebel fleet hasn’t taken over the repair beacons.

A few things you will really want: maxed out shield, level 4 engine (anything more and you probably won’t have power for it), at least rank 2 stealth, either a level 3 teleporter with lots of mantis OR a lot of firepower/bombs/missiles/ion.

First Stage
The first fight may be intimidating, but it’s a fairly traditional fight. The boss has four weapons, each with its own system. From left to right, they are ion burst (3 shots), laser burst (3 shots), missile burst (3 shots) and a beam weapon. The systems for the four weapons are manned by a single crew each, and are not connected to the main body, so the rest of the crew can’t help or fix the system. The ship has 4 shields, a very large crew (who will not board your ship in this stage), and a stealth system. Obviously the first things you want to take down are the missile and ion.

Boarding-focused
If your ship is heavily invested in boarding, then the first thing you want to do is to teleport 2 of your mantis to the weapon system for the missile burst, and then another 2 to the ion burst. Once the systems are destroyed, teleport your mantis back, take out beam, DO NOT touch the laser weapon. Make sure that the crew manning the laser weapon remains alive. You’ll see why soon.

Now focus on the rest of the ship. The goal is to kill the entire crew except the lone guy manning laser. You should use bomb/missile to destroy the med station on the ship, teleport your mantis in, and teleport them back at low health. IMPORTANT: while the Flagship is in stealth, you will not be able to teleport your crew back, so you may want to destroy the stealth system as well. Keep on teleporting back and forth, keeping their med and stealth down. Level 3 teleporter will be essential here, and the healing bomb can be very helpful.

Once the entire crew is dead, except that one lone guy, proceed to destroy the shield from within and the hull. The reason that you must leave one crew alive is because a) although the ship repairs its systems between Stages, the crew carries forward; b) if the entire crew is dead, the ship becomes an AI ship, and all systems automatically repair themselves, the subsequent fights will become nearly impossible.

Weapon-focused
If your ship is heavily invested in weapons, then I hope you will have either a lot of good missiles/bombs or a lot of ion weapons. If you have two Ion Blasters (especially Mk2 ones), autofire those on the shield and the ship’s shield should be locked down within a few second. Proceed to destroy missile weapon, the ion weapon and the beam. Make sure that the laser remains untouched, the crew manning the laser must be alive. Alternatively just spam missiles/bombs at the three weapons until the weapons and the crew are both down.

Once the ship is mostly harmless, proceed to kill the rest of the crew, except the one person manning the laser. I recommend breaking the medbay, set it on fire, breach its hull, use small bombs and watch the crew rushing to it one by one to be roasted. The reason that you must leave one crew alive is because a) although the ship repairs its systems between Stages, the crew carries forward; b) if the entire crew is dead, the ship becomes an AI ship, and all systems automatically repair themselves, the subsequent fights will become very annoying. When all has been done, destroy the shield and hull. Don’t use too many missiles, you’ll want a good stash for the next two fights.

Second Stage
In this stage the ship will lose its stealth system and ion weapon. All other systems will be repaired to full, but the crew will remain the same. If you’ve done everything correctly, then there should only be one poor sucker manning a laser, trapped between 2 squares. This time around the boss will focus on droids. The boss will send boarding droids onto your ship. Don’t bother killing them, the boss will just send another one if it’s dead. There will also be a new mechanic called “Power Surge”. When a “Power Surge” is happening you will receive a warning similar to solar flares. In this stage the Power Surge comes in the form of 10+ anti-ship/beam droids spawning and ripping your ship apart. Power Surge droids will spawn and function even if the flagship’s droid control system is down.

Boarding-focused
Send 2 mantis to the droid control system and 2 mantis to the rocket. Ideally your ship should at least have a few doors to keep the droid occupied while the systems are being damaged. Once the rockets are down, and the droid control is damaged enough for the boarding droid to go offline, head to the shields and engines. Tear those apart and the ship will be fully defenseless.

While your boarding crew is working, your ship needs to survive the Power Surges. The spawned droids will last awhile, so you will want to time it carefully. Don’t hit stealth as soon as the warning shows up, instead you should only stealth when you see the spawned droids starting to fire. Level 3 stealth will of course make things easier.

Weapon-focused
Pretty much copy-paste First Stage strat. Ion-weapon lockdown shield, destroy droid control and rocket, or use missiles/bombs. The more important part is to survive Power Surges. You will want to time it carefully, since the spawned droids last awhile. Don’t hit stealth as soon as the warning shows up, instead you should only stealth when you see the spawned droids starting to fire. Level 3 stealth will of course make things easier.

Third Stage
In this stage the ship will lose its droid controls and the beam weapon. In this stage the ship will now have a somewhat powerful Zoltan shield, and start migrating its entire crew onto your ship. Fortunately they are all dead, except that one guy who can’t reach the teleporter anyway. The Power Surge in this stage comes in two forms: it will either fully restore the Zoltan shield, or it will send out a barrage of lasers at your ship (around 10 bolts).

Boarding-focused
Throw everything you have at that damn shield. If you don’t already know by this point, you can’t teleport into a ship while the Zoltan shield is active. Once the green shield is down, teleport your mantis to the rocket and destroy it, then to the shield and engine.

The Power Surge is easier to dodge than Second Stage because it doesn’t last nearly as long. Even rank 1 Stealth should be sufficient. Again, time it when you see the barrage of beams firing, not when you see the warning. Indeed, you may not want to use high ranking Stealth at all. Since those stealth last too long, their cooldowns start later than rank 1 and you may not have stealth available when the next wave of lasers are coming.

Weapon-focused
I guess it’s starting to become rather obvious that Ion-lockdown is pretty OP. Do that to the shield again, then destroy rocket and engine.

The Power Surge is easier to dodge than Second Stage because it doesn’t last nearly as long. Even rank 1 Stealth should be sufficient. Again, time it when you see the barrage of beams firing, not when you see the warning. Indeed, you may not want to use high ranking Stealth at all. Since those stealth last too long, their cooldowns start later than rank 1 and you may not have stealth available when the next wave of lasers are coming.

Conclusion
Per design Stage 3 is supposed to be the hardest. Indeed on my first playthrough where there was poor planning, my ship was quickly overran by 8-10 boarders tearing my ship apart from the inside. With knowledge of the fight and proper planning, the final boss is arguably easier than some dice-blessed enemies you may run into (i.e. mantis ship vs autoship with 4 shield and rockets).