The game uses a time/phase system. Every phase consists of 10 turns. After 10 turns, the next phase begins. One turn is used when you go to one mission on a map, or return to a base. If you get shot down, it also uses one turn. At the end of a phase, the game will look over the missions you completed and dole out the new ones taking into consideration the current circumstances. The ones vital to the war have to be completed, as if you haven't finished them, HQ will prompt you to bring those to a close at the start of a phase. Thus, getting shot down repeatedly and returning to base will sorta have you "missing out" on more missions.
If you do finish all the missions in a phase, and have leftover turns, all the remaining missions in the phase will be "standby" (dogfighting) missions until the end of the phase.
If you want, you can advance "time" by "resting" in your quarters (the room that you view your stats in). It's an interesting way to get you to do well because if you finish the missions and get more standby missions, you can get extra cash and I don't know what else. If you noticed, every phase brings about new responses by the characters such as the sit rep by Amelia, as well as the talk in all the different places by everyone. You can observe the phase and turns at the base menu screens. If you get shot down a lot, you can instead reload your save(save after every completed mission) and thus, won't use up your turns since you lose turns every time you get shot down (1 to go there, 1 to go back).
It's a little confusing at first, and I probably didn't explain it as easy as the manual did. I shoulda just copied the manual's explanation.
I am also wondering if completing the game in a certain number of phases or turns will also play a role in unlocking characters...for instance Ellen, whom no one has been able to figure out exactly how she is unlocked, though many surmise it has to do with shooting her and Albert down with Ken always. Some people said they have done that and still not gotten Ellen.