They will do an investigation and likely charge you for them, unless they think you stole them, in which case they may bring charges against you. None of us can guess with any certainty.
This post is for information purposes only and does not constitute legal advice, nor does it establish an attorney client relationship with Mr. Cassara.
I agree with Mr.Cassara. Normally, they will have you fill out a missing gear statement and perhaps do an investigation because of the high dollar value of the plates. However, if they believe that you stole them, they could certainly investigate you criminally as well. If you are at Camp Lejeune, many people are trying to sell their SAPI plates on Lejeune yard sales, and other places. There are also many theft allegations stealing and selling SAPI plates going on around Camp Lejeune as well. If anyone reads you your rights, make sure you invoke your right to remain silent and exercise your right to speak to an attorney.
It certainly sounds as if the command was able to substantiate the alleged misconduct. Did you take NJP? Not sure where you are in the process. If you are still in the investigative stage then the command can put you on legal hold until disposition of the allegations. If this is the case you should seek legal advice from the detailed defense shop on base or call a military defense attorney for a free consult. Please read my Avvo profile and call when you are ready.