I drastically bumped up the difficulty on the Defend the base mission, since the first time I got there, the base had killed off all the enemies before I arrived
Now its less of a starbase and more of a small battlestation or large space station.
The base should be able to help out a little bit (Try hiding behind it to reduce the fire hitting you).
During my test, the base was barely holding off the cruisers that were attacking it, but it could only kill the fighters and destroyers.
I used my torpedoes to disable the shield generators on any nearby enemy cruiser I could hit without getting myself killed, and let the base finish it off while I repaired.
The Dagger mission is actually supposed to be impossible. There originally wasn't even any plot coded in for a mission success (possible to achieve using cheat codes and lots of luck in unmodded SF).
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For missile defense, you'll need Point Defense
Cannons. The lasers are only good against fighters.
Do watch out for Ion mines, it sounds like you'll hate them as much as I do
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As for AI, I don't really know.
I've only dabbled a bit in AI modding for SE4, and even less for SF.
I'm more of a physics modder.