The major legal action in the Navy always has been the general court-martial.  In practice, such a court is preceded by a court of inquiry that determines if an alleged offense is, in fact, present and prosecutable.  In her long history, "Old Ironsides" has had two captains who have been involved in the process, one who was the subject of a court of inquiry and another was court-martialled.  Detailed records of the cases is presented here.

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Court of Inquiry on Captain Charles Stewart (1814)

Court-Martial of Captain Jesse Duncan Elliott (1840)