The trick to beating the final boss is to have maxed teleport and cloaking. This lets you avoid all missile volleys, by cloaking just before the first few would hit and boarding the missile weapon system to disable it. Also you should murder all but one of the crew during the first battle (this is tricky, but you can take your time), so you can disable systems quickly in the second and third battles without them being repaired.
Cloaking and teleporters are great early investments, too. Cloaking saves tons of resources that would have been spent on repairs, and killing the enemy crew gives better rewards compared to blowing up the ship.
Oddly enough, I only ever made it to the final boss twice. The first time was with the stealth cruiser, which had maxed stealth and teleporting, and I got annihilated by missile volleys and those combat boarding drones.
The second time was with the Engi cruiser, and I handily beat him. I had only EMP weapons, a level 2 defense drone, and a level 2 attack drone (probably also a repair drone). I just played damage control and set the EMP weapons to autofire at the shield room. When they eventually disable it, the level 2 attack drone shredded him.
Haven't played since then (figured I'd quit while I was ahead), but this may get me back in.
How did you get that far with the stealth cruiser? I love playing the ship but I never survive past sector 3. I have logged hundreds of hours on FTL and never once beaten it with my favorite ships :(
The stealth cruiser is definitely hard to work with, and requires very precision timing on the part of the player. It's a tough ship to win fights with if it doesn't have the ability to outright destroy or cripple it's enemy as it comes out of stealth, which is why I had trouble in the final encounter.
First and foremost, it is tempting to get shields working early on, but I actually had better luck upgrading stealth first and then shields - early encounters can be destroyed before they fire at you if your weapons loadout is good. But be sure to upgrade to full shielding before getting to the end.
Basic idea for me was to charge all my weapons to full, fire if I had an opportunity to before the biggest enemy weapon, and wait for the largest enemy weapon to fire (usually a missile). As it fired, engage stealth. This gives you a really absurdly high dodge chance, and the weapons fire almost always misses.
Immediately drop stealth and fire all weapons. If the ship has a lot of shields, target shields, otherwise target weapons (none or low shields means you will hurt bad if they fire back). Generally this can cripple the enemy ship, making it so they can't effectively engage you - this is pretty vital to keeping the stealth cruiser alive. If it starts to go bad for you, stealth away, and consider leaving the engagement.
For what it's worth, my best loadout consisted of a large missile system for punching through shields to disable the shield system, an EMP bomb system for disabling defensive drones (or other systems), and a fire beam weapon I used to try and hit shields and weapons at the same time, all on an alpha strike after coming out of stealth. I also had a teleportation rig set up with two of the insectoid crew that could take the fight to the enemy - this was really useful at keeping them busy, and keeping the ship alive. Also good for when I ran out of missiles - could send them in to disable shields and / or weapons and get out.
I still got torn up by the drones sent in by the final boss though, so a good drone defense system would have been invaluable - if you stealth, they just hover around until you come out of stealth, then breach. Good luck. :-D
I basically did the same thing except my volley out of stealth went for the weapons instead of shields since I wanted to make sure it couldn't hurt me after my cloak wears off. Perhaps I should start running from less than optimal fights, usually I stick out every fight because I want all the scrap.
Yeah, targeting weapons is a great idea if the enemy has low enough shields (based on your weapons load) that you can punch through them, disable weapons completely, and then do the same for the shield, while they sit there unable to shoot you, scrambling to repair.
The problem the stealth ship has is when the enemy ship has shields and weapons in abundance (those Zoltan ships are EVIL). In this case, you have to take the harder task (and almost always take damage) and knock out shields first. I loved the long beam weapons because I could drop shields for a moment and burn apart weapons and shields on most ships.
Another important thing I would always do is not fire missiles if shields were down unless weapons were still up - you will need every one of those missiles later.
Not my approach. Maxed engines for evasion, masses of lasers, and it goes down pretty quickly. Like others have said, there's more than one way to do it.
I beat the final boss the second time I met it, without teleport or cloaking. I had maxed shields, nearly maxed engines, and a fuckton of lasers. Cloak and teleport are fantastically useful, but despite what everyone says, there is no "required" kit to beat the boss.
Cloak can't be bought on some ships. Some ships have extremely bad crew for boarding and don't even get to get some better crew. There's certainly more than one way to win it.
There are a number of ways to carry out a similar strategy, ie: kill all crew except one and destroy subsystems before trying to damage the hull.
The only ship that can't equip Cloak it is the Federation Cruiser (and its variant) and this ship has the Artillery Beam to make up for it. As for crew, between Stores and Slavers it's entirely possible to get to Mantis or, even better, two Rock crew members before facing the boss. This, at the very least, will let you take out the boss's weapons.
Cloaking and teleporters are great early investments, too. Cloaking saves tons of resources that would have been spent on repairs, and killing the enemy crew gives better rewards compared to blowing up the ship.