In the mission were you have to face the 8492 Squad yes it would be nice to kill them but don't just run away from them in the degree that the game tells you to (look at the map and you will see a dotted line that was not there before this mission.) Go that way but don't wait for your team mates(wingmen) they never die. Just press the R1 button and go as fast as you can the 8492 Squad will send a missle or 2 at you every now and then just shake them off (go up then down then up until the warning is gone)and keep going once you meet the line you will have a Successful mission.
Actually, you don't have to 'keep playing the missions'. The missions are chosen by the answers you give when chopper asks you about the song 'face of the coin'. Say yes and you'll do the top mission/s say no and you'll do the bottom. Simple huh?