Hello again and thank you for the additional information although there are still some facts missing since there has to be a connection between the scratch and underage drinking for him, that would have warranted him even being questioned and charged. Also, it is relevant what "on the back" of the ID was scratched. That is why I asked about what specifically was scratched out. If the DOB, then that might be the issue that even got the attention of the Command. The issue with his roommate, in the Command's viewpoint, is likely that they were both engaged in the same behavior or that your son knew what was going on. That I can't guess since I don't have the file in front of me and the facts in possession of the Command. Unfortunately, neither of us do, and your son only has the facts that he knows and not from the Command's perspective.
In any event, he can, and should have already, gone to speak with the local judge advocate office that assists in personal representation and defense. They would have counselled him about his rights, in particular is right to refuse NJP
(Captain's Mast.) Since he is not attached to a ship, he can refuse it. However, that means that then the Command could refer his to a court-martial if they think they have enough evidence to prove the charges beyond a reasonable doubt. At Mast, the Captain must just believe that the evidence supports the charges by a preponderance of the evidence, which is less that beyond a reasonable doubt. That is because this is an administrative hearing and not a criminal trial.
Your son, has the right, but does not have to, make a statement at Mast and present any evidence that he may have to support his position.
If the Captain does award him punishment at Mast, he can appeal the findings to the next level up (the Admiral) and the Admiral's judge advocate will review the case for sufficiency of the evidence. They can set aside the punishment or uphold it. If they uphold it, then that is the end of the process.
If you have any specific follow up questions, please feel free to ask them. I would be glad to assist you further if I can.