Stop upgradeing the "Darkstar One" at level 10. Seriously.
The game scales what it throws at the player by the DarkStar One's current level. In the FLAK missions it forgets to also upgrade your FLAK turret to deal with the higher number of enemies. With a level 10 ship the the drone swarms will number 5-7 ships, with a few three ship swarms. Should finish the mission with the turret at ~50% health.
In fact, the whole main story line can be done with a level 10 ship with the game Difficulty set to 3. It's not really that hard. The Artifacts are not going anywhere and you have a reason to keep playing after the plot.

Wow that is just crazy, basically this makes the whole RPG element of the game redundant.
Thanks for the tip I'll bear it in mind if I get stuck at some point.

Tried that : For some reason, it's now a lot harder still O_o....I barely last 4 waves instead of 8-10 with a [to that time-point] fully upgraded ship...
Finally found that Mesa-Mod and used that....and it's ludicrous how opposite it takes it....a 2 year old can shoot 1 Thul Drone every 35 seconds :-\ Not to mention that going back to "original" mode to continue the game seems to have been nerfed to mesa-mod standards "Oh, there's 7 pirates attacking!" *1-2 attack*
"Now there's 3 bodyguards coming in!" *1 appears*
I'm now very disappointed in this game :( Right upto that one mission, it's exciting, it's mindless, it's good. I can even tolerate the inane blather of everyone you talk to...or fly near.

i was quite scared from all that reading about the dreadful FLAK2 mission, but it turned to be quite easy. Took like 5 attempts to finish it with a level 17 ship on difficulty 4. I think the prob people have with is that the cannon must not fire continuously, but spend some time waiting to regenerate ammo. That is, not fire-wait-fire-wait. But fire-fire-wait-wait.

Okay, this must be why I've got a problem with saving Captain Hornblower. I made my own little mod just to allow myself to upgrade the ship fully by the end of the game. I've got a level 22 ship and Hornblower gets blown away almost before I get to even target my second pirate. Considering you don't even auto-target Hornblower when you enter the system, so you can't hit "Y" to help him (and target a pirate ship), and the pirate ships are all "green" when you enter (so hitting "R" doesn't target them, either).

Is the game increasing the number and power of the enemy ships without increasing Hornblower's (or other "friendly" ships) power?

For the sake of being able to save this ship and those stations, do I need to restore back to when I had a level 10 ship and play the game from there, ignoring the artifacts and better equipment till I get past the second Flak mission?

PK

Hii i managed to complete flak mission 2 in my first attempt with a level 8 ship

The game difficulty does seem to be dependent on the level of darkstar 1.