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Since the agency did not comply with the request for final agency decision time limits, you need to write to Sec Navy and request the matter be closed in your favor. If the agency/Secretary of the Navy does not close the case in your favor, then your next step is you can file a suit in the US Court of Federal Claims against the agency asking the court to close and dismiss the case against you.
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Okay, thank you for clarification.
In that event, since you have no response within the time provided, you have the next step of filing suit in the US Court of Federal Claims since no final agency decision was rendered and then you take them to court for your discrimination claim, for which I would strongly urge you to use a local discrimination attorney for representation.