My new story is about a covert operations squad in the U.S. army called the Reaper Company. They have been given a mission to assassinate the leaders of a Muslim extremist group by the General. However, in the middle of the operation, a retaliation on American soil occurs. Immediately after that, the members of Reaper Company begin to die outside of battle, leaving only the head of the Company, Reaper One. He begins to suspect the extremists, and finishes the job given to him by the Supreme Commander... this is where I am stuck. I was considering making Reaper One discover that the S.C. called in the attacks on his company, but I decided against that... now I don't know where to go with the story. Help?
He has completed his objective, so he must follow his orders to return from his mission or proceed to the next one. Unless there is a reason he cannot follow tjose orders, his course is set. So you need to create an obstacle oreventing him from following those orders, either because he is unable to, or because he believes those orders are illegal. If he abandons his orders, he is subject to court martial. If he can demonstrate his orders are illegal, he can prevail in the trial, and in fact to knowingly follow an illegal order is aslo a court martial offense. If he is unable to follow his orders, whatever he learns in the process can advance your plot. But he is still bound by his orders. To voluntarily deviate from those orders is to break military law, so for him to do so, it must be of greater importance than the consequences of disobedience. Does that help at all?
It does, a lot in fact. You've pointed me in the right direction, now I just need to iron out the specifics. Thank you.