Most likely the commander will issue an MPO if recommended by the FAP as part of its review of the case.  However, if you are not granted a MPO, you might still be eligible for a civil protective or restraining order issued by your home state, or the state you are currently living in.  Unlike civil protective order proceedings, there is no real appeal process in the Military if you are denied an MPO or if you disagree with the decision of the commanding officer.  You can seek assistance in a variety of ways if the MPO is denied, and you can continue to inform the commander of further abuse, but you cannot "appeal" the decision. 

Visit the Restraining Orders page for your state on this website to find out if you may be eligible for a civil restraining order.

Please note that even though there is a law requiring military bases to enforce protective orders and civil restraining orders, this law may not be fully enforced.  See Are MPOs and civil protective orders (CPOs) valid where ever I go?