You're talking about Operation Gamma, Flying Blind is just a task within that mission.
Ignore the fighters, take out the worker bees first. Then take out the fighters. I think there's 3 rounds of this. The worker bees aren't invisible, just really tiny. You can use the "tab" key to flip through targets and find them if it helps, but they hang out by the nodes you need to disable.
the fighters keep destroying me while I'm getting the bee
do you need a special ship?
No, the ship doesn't matter. Its usually equipment. You could try temporarily moving your shields from your starship to your shuttle for that mission. You could also skip the mission. Either that or find someone of a higher level to play through it with you. Are you a part of our fleet (or any fleet)?
Whenever I do a shuttle mission, i always move most of my gear from my starship to my shuttle. It definitely makes a difference.
And specific to this mission, as Attilio said, kill the work bees first, then go for the fighters. I had a LOT of trouble with this one until I figured that out. It may take you a few tries, but it's definitely beatable.
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I'm shooting the worker bee and by the time I've got it dead, my shields are gone and I'm down to 35% hull then they fly into me and commit suicide to finish me off.
I always take the best of my starships gear.
Also I use Beam arrays and slot FAW with an autofire macro.
Also have a satellite equipped in devices that you can use to help you fire - it will also take some of the threat from you.
I used to have awful trouble with this mission - but the rewards are good.