Now after my first "yayiwonthegamewaitwhatarrrrrgh-deleteFTLfromgamelibrary" moment in the above thread,
I've decided not to focus on beating the boss, but rather unlocking some ships.
My first goal was unlocking the slug cruiser, but that didn't go so well...
2 encounters I've let the ship get away, and once beat the ship, but forgot that i had click the wrong option.
Sorry if I'm getting off track. Anyways, In another attempt to find the illusive slug cruiser,
I took the good'ol Torus for my ship.
I found the drone recovery arm ON MY FIRST BEACON. FOR FREE

After a few sectors, I had the luck of finding a free ion bomb and a breech misslle after that
(which I didn't have enough power to arm it).
Sector 7, No hull-damaging weapons except the Anti-ship Mark 1, I was a bit worried.
I had no scrap to upgrade my weapons, So my only option was to find a Anti-ship drone
before the last stand.
(And I also completely forgot about the slug cruiser at this point)
I had no luck. But guess what happened next?
The store in the last stand just decided to have a Anti-ship drone in stock!

So before the battle, my ship was fitted with:
3 Shields
3 Engine bars
Level 2 Teleporter
Level 2 Cloak
Weapons:
1x Ion Blast 2
1x Ion Bomb
Crew:
3x Engies (One died during stage 2. RIP Notch.)
2x Humans
2x Mantis
2x Rockmen
Stage 1. Was quite easy. Autofired all my ion stuff into the shields, Teleported my mantis crew into the misslle room, and the drones finished them nicely
Stage 2. Now this was tricky. repeated the same step as stage 1 but the power surge
almost made me think that i lost the ship. Luckly it didn't. Survived with 5~6 hulls.
Now by this time I had an important decision to make. I had to go to a repair bay to even have a chance at killing the boss. But 2 of the 3 repair bays were already under rebel control.
The last repair bay was at the upper left corner on the sector.
I was at the bottom left.
I made a run for it. got my hull back up to 20 something points and was back on track.
and with the flagship 1 jump away from the Federation base, I made it.
Stage 3. This is it. all those FTL Let's Plays on Youtube, reading all those forum posts,
It was all for this moment.
Stage 3 wasn't as hard as I thought though, after a few blasts of missed lasers from the "Super weapon" The boss was down.
Phew.
Well, that's it for the story,
and if I had one word of advice to those who seek to hunt the boss:
DON'T PANIC.
Seriously. It's the most important lesson I learned after 54 broken ships.
Thanks for reading, and best of luck to you all.
I'm off to take the Osprey for a spin.