He hasn't beaten it, user. Which means he probably hasn't unlocked much, and if he can't beat the Flagship with the normal ship, then he definitely can't get there on a Stealther, that shit's even more micromanagement and complex.
Why didn't they just FTL jump into the flagship?
git gud
Or just try to jump as many time possible each sector, to maximize scrap and weapons.
Why is this cockstopping game so difficult on Hard? Other Roguelites give me little trouble after 100 hours but this shit is demanding.
Don't play on hard
Your ship needs to be capable of getting rid of 4 layers of shields and destroying the missile launcher at the very least. Easiest method to kill the guns are to use a teleporter. Having hacking is an easy way to remove shields. Don't bother going for 4 shield layers, go for more engines, 45% is usually good.
Get Hacking, it's OP as fuck. If you power it down the instant a defense drone shoots it the Hacking Drone stops moving, just power it up again after a second and the laser will miss. Hacking 2 will let you drop 3 layers of shields, and will get you all the way to sector 6-7 Hacking 3 drops all 4. Combine that with beams for easy mode.
FLAK CANNONS
Pause
Because the flagship is piss easy. Literally just keep the missle launcher down.
Play the tutorial
I understood that reference