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What is her MOS?
I ask because there may be a concern if she is married to you and is required to hold a certain level of security clearance.
They are also possibly concerned about you entering base.
They're allowed to ask her about her relationship to someone that was convicted of possession of child pornography if they view the relationship as pertinent to her job or the safety of the base.
If they are continually asking her about it, and it rises to the level of harassment, she can file an Art 138 complaint with her command.
Sort of. They may ban or prohibit from entering anyone they wish as long as the grounds for doing so are legal and tied to the protection of the base and persons within. The base commander could, for example, ban anyone convicted of possession of child pornography from entering his base.
Also, the security clearance investigation is not performed locally. It may be that the local command just found out. And while I don't know if this is why, they may be probing to determine whether to revoke her clearance, or to ban you from base, or both.
Or, it could be that someone found out about your relationship with a person in the Navy, was concerned, and contacted the command with a request to look into it.
It this point there a many uncertainties. If the questions persist, and rise to the level of harassment. She can file a complaint. Until then, there's not much to be done.
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