The Rebel Flagship: The Final Hurdle of FTL (Best Boss Battles)

FTL: Faster Than Light is one of my favorite indie games of all time. Whereas other roguelike games I find more frustrating than entertaining, when I play FTL, I often find myself doing four or five consecutive runs, regardless of the success of any given one. It’s challenging, it’s satisfying, and it’s freakishly addictive.

The concept of the game is simple. You are a lone ship on the run, fleeing from the ever-approaching rebel army to warn the galactic federation of their coming attack. Along the way, you’ll come across all kinds of random events in which you can either upgrade your ship, gain new crewmates, or suffer horrible tragedy and die early.

If you survive it all, you get to face off against the most powerful ship in the game: the Rebel Flagship.

The ship that caused me endless grief in middle school… I still have nightmares sometimes.

This absolute monster of a ship is far and beyond anything else you’ll encounter in this game. If you aren’t fully prepared with as much armor and weaponry as you can get, you’ll never overcome it. Even if you’re armed to the teeth, you might not survive. If you don’t know what you’re in for, you might just get annihilated before you even get a chance to fight back!

The fight is split into three phases. The first is the most straightforward: the flagship will bombard you with all of its weaponry. The ion cannons will disable your shields in the blink of an eye, the plasma lasers and missiles will blast holes in your hull and annihilate your ship’s systems, and the laser will cut you to pieces for massive damage. It’s ruthless, but if you stay on your toes and keep the weapons disabled, you ought to survive.

Now, if you’re playing on the Advanced Edition, things are much trickier. There, the first phase also has access to Hacking. With this, the Flagship deploys a drone that locks down one of your ship’s systems entirely, rendering that useless. Depending on the system chosen, this could be devastating, leaving you defenseless or unable to attack or escape.

Because of course they had to make it harder.

Phase two is even more brutal. The damage to the ship done in phase one may have destroyed its ion cannons, but now you’ve got to deal with enemy drones. If you don’t have anti-drone systems or take the Flagship’s systems down fast, you’ll soon be overwhelmed by a veritable horde. Oh, yeah, and the Flagship is still shooting at you.

It also now uses a new ability called Power Surge. With this, the Flagship unleashes an intense volley of blasts, shooting upwards of half a dozen shots at you all at once. This is set to a timer and you’ve got no way to disable it. You’ve just got to power through however you can.

The third and final phase of the fight is by no means easy. The Flagship further upgrades its shield systems, making it difficult to get any damage through until you remove the buff. Now, when Power Surge activates, said shield buffs are restored. All the while, the Flagship continues to bombard you with missiles and laser shots.

On top of all of that is the crew. See, the Flagship has a teleporter system that allows it to send its crew over to attack yours. If your crew isn’t battle-ready, or your ship’s doors aren’t shorn up against intruders, then they may very well kill you from within.

Oh, and that reminds me: if you want to use that strategy against them with your own crew, it won’t work. Turns out, the Flagship gets taken over by an AI if you kill the whole crew. Because of course this evil thing would have Skynet installed on it!

With how customizable your ship is in FTL, how you approach all of this is up to your own play style. That, and luck; if you don’t get the upgrades and items you need throughout your journey, there’s no way in hell you can beat the Flagship, regardless of your chosen style. But with enough luck and mastery of your chosen play style, you can overcome it!

Of course, some strategies are going to be easier than others. A ship with lots of shields and missiles will have an easier time than a stealth ship that teleports its crew to attack the enemy from within. There are strategies out there online that can trivialize even this monstrous boss battle.

But I’d strongly recommend against looking up a guide. Part of what makes this fight so cool is finding a way to beat it with your own build. Finding a way to overcome the challenge with your own rickety ship and its crew of alien freaks is immensely satisfying.

And incredibly heartbreaking when said rickety ship and alien freaks get blown into space dust.

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