Damn, was that a struggle :P It feels like there's a massive load off of my shoulders!
Since I uninstalled the game last year in disgust it has been nagging at me to at least manage one successful run. In retrospect, the biggest mistake I made in my whole string of unsuccessful attempts was to spend scrap to quickly to level my ship, and then not to be able to buy what I wanted at stores.

Have to say though, I'm not sure whether this run I just did counts. I had incredibly good luck. In particular, and this will probably never happen to me again, I found a weapon pre-igniter in the 2nd sector during an event. That's just crazy good fortune.

Congratulations!
Don't downplay your success, though! Everyone gets lucky, but ultimately you won because you persevered, learned from mistakes, and used some good strategies.

I've always felt that beating the flagship is one of the best accomplishment you can have on your gaming resume.

True! Especially on hard... ;)

Irrespective of the level you beat it on though - congratulations!

ty ty :)

It's all the way up there along with landing on Mun for the first time :D

EDIT: Getting the hang of this now - twice in one day! 2nd one was with the engi ship. Cloaking and mind control ftw!

The real flagship to beat in this game is your own sense of frustration at losing. Kill that one and you've got hundreds of hours of rich gameplay discovering new ways to do better and how best to use whatever it is you were lucky to find or be unlucky enough to get stuck with.

General pointers I figured out from losing 100s of games and winning a couple dozen:

* Think like a Ferengi. Winning is counterproductive if it costs you more in repairs, missiles, and drones than you got in profit. Learn when to cut your 1-fuel loss and bail. That typically means risking more than 2-3 damage isn't going to be worth it if you don't luck out with a nice bonus weapon or crew member. Your goal in this game is to maximize profit by hitting as many map areas as possible before the rebels show up.

* Shields to 2 ASAP. The difference in repair costs is huge for the first 3-4 maps or so and you'll often be invulnerable, making it easier to capture or defeat cheaply, without using drones/missiles. I try to finish map 1 with 100 scrap with this in mind. If starting with a stealth ship, target stealth 2 + a shield module or stealth 3 if you have trouble finding one before the end of map 2.

* Long range sensors are the best thing you can buy for 30 scrap.

* Weapon Pre-Igniters are the best thing you can buy.

* Defense Scrambler might also bet the best thing you can buy if it's likely there's enough game left to find a hacking module or you already have one. HM's are insanely versatile, often plugging ship build offense and defense gaps you didn't even have. You can use it to capture without raiding, strip shields, delay the other guys weapons, turn infirmaries into death chambers, all while (often by accident) isolating crew members from important stations, fire-fighting efforts, or mantis raiding parties. Or if you really want to isolate them lock all their doors.

* Start small with weapons with a recharge time of 12 seconds or less and use no ammo. When you can penetrate shields reliably, beams are a no-brainer. Only go big early if you luck out with an early pre-igniter. Cloak ships can afford medium size weapons like Halberd beams in the early game but try to mix with smaller stuff.