I've got some odd theories about this fellow. He's a fun character to speculate about, and MM in general is rich with theorizing potential, so bear with me as I try to explain my theory.
Judging by the HMS's actions, I'd say that he's more than human, possibly a mini-deity of sorts, or at least with greater connections to the divine than the average individual. His jerky motions, pulling an organ out of midair, disappearing into thin air at the end of the story, hardly attributes of a normal human/hylian/terminian. At the very least, he has some sort of odd power, not to mention that, from my perspective, it seems that the HMS pulls Link back in time if Link fails to stop the Moon from crashing. If you watch the Moon crashing cutscene, after Link gets engulfed by the flames, he just whites out, then we hear "You've met with a terrible fate, haven't you?", and suddenly find ourselves with the HMS, who's cheerfully reminding us of the 3-day limit. No Game Over screen or anything. I don't know about you, but I've always felt that the HMS somehow pulled Link back in time to save him.
Now, there's also the fact that he is in possession of Majora's Mask before the game's start, and he seems oddly nonchalant about it being stolen at first. At least, he doesn't seem as panicked as he should, and he doesn't go off trying to get it back himself. In fact, he even seems to have been anticipating Link's arrival, as if he knew Link would come and get the mask back for him. Now, I subscribe to the theory that Termina abandoned faith in the Goddesses and was therefore forsaken by them and doomed to die, yet by either divine mercy or something to that effect, some higher powers decided to give Termina a second chance at redemption. My personal theory is that the Skull Kid, feeling abandoned by the Giants, would be a symbol to the Terminians, who abandoned the Goddesses. If the Skull Kid could overcome the Mask and reconcile with the Giants, then Termina could overcome the Moon and learn to reconcile with faith. Now what does this have to do with the HMS? Simple. The HMS would be the Goddesses' messenger. He would take the Mask down to Termina, guide the hero Link into this adventure (since every doomed world needs a hero), and protect him should he fail (pulling him back through time if the Moon crashed). I found it awfully peculiar that the HMS was relatively calm about the Mask being stolen, yet absolutely maniacal at Link's initial failure to retrieve it. Maybe he was expecting a prophesied success and was outraged it didn't happen immediately.
*shrugs* This is all personal speculation built around my observations of his behavior in-game. I hope it wasn't too confusing to follow. Also, in regards to the Manga adaptation, I don't consider the Manga storyline canonical enough to override in-game evidence. The HMS was seemingly evil in the Manga when he was clearly benevolent in the game, so I'm not inclined to use the Manga for my theories on this fellow.