I'm playing for the first time on my Mac and can't figure out how to change the difficulty. How do I do it? I haven't beaten the third mission yet (I read something that seemed to imply that difficulty needed to be unlocked).
From the game manual: "The mission selection screen also shows you three boxes that indicate if you were previously successful in battle on medium, hard or expert difficulty. There is no ‘easy’ option. If you wanted easy, you should not have signed up for the space navy and you are not fit to take command of a fleet of Andromedan space mites."
The difficulty can be raised for each battle at the deployment screen. Harder battles bring more honour.
As for the third mission, design your own ships. Anomalies here lower everyone's shields and prevent deployment of fighters, so you might concentrate on armor instead. Dedicated anti-missile frigates might be worth considering. Remember to set orders to your ships. Clear their frigates first as they are easy to bring down. Concentrate your fleet to one corner of the map, use a decoy ship in the opposite corner to divide the enemy force.
It's on the bottom middle of the deployment screen.