great. so now i get to shove story down the players throats.
i suppose i can dig that
Only if you lack imagination.
You can't have optional objectives listed but you can make alternate options that aren't expressed in the objective window. I've seen quite a few that leave the "how" up to the player, instead of forcing a player down a particular railroad.
Would love to see some kind trigger effect so once you compete it something happens. fix all the damage parts of ships the red alert turns off. beam the people up 1st and you get to few patrols. The ability to remove or add things to the map would nice. So you get a perk for doing them.
A easy way to solve this problem would be to implement a condition to missions and give a virtual emblem or so. So you need to have done mission part 1 to be able to do mission part 2a or mission part 2b depending what choice (emblem) you made in mission part 1.