Without knowing the specifics of the case, it's not possible to tell who initiated the commander's inquiry. It could have been their direct unit commander, or it could have been an officer in the higher in the chain-of-command. But, given the fact that they refused Admiral's Mast, it's quite likely that it was indeed a General or Flag officer that initiated the actual Article 15 proceeding.
The SEALs refused Mast, which is their right, so the Admiral (in this case a US Army MajGen) convened a court-martial.