Since my completion a few months ago, I've visited several (very long) story analysis and whatnot, and the plot is indeed...deep.
Basically, Emir is literally just a guy. Then, at some point, he gets spiritually resurrected/awakened by Kun Lan after an incident where he kills some people at Coburn Elementary. Long before the incident at the Union Hotel, he is just a normal guy, then he kills some folks, then he is awakened by the Devil (symbolically).
The Smith Syndicate are 7 separate people. The six (Dan, Con, Coyote, Kaede, Kevin and Mask) are normal people killed in battle, resurrected by Harman, and then recruited to fight for Harman. Harman and Kun Lan both have resurrecting capabilities.
AND THEEEEEN Emir (for some reason) kills the entire Smith Syndicate at the Union Hotel! He goes to the roof where Harman then proceeds to assimilate the dead Smiths INTO Emir, and once again, Emir is spiritually resurrected as Garcian Smith with supposedly no memory of his previous life. Thus, the Killer7 is born.
How IN GOD Garcian seems to experience these events like some sort of flashback at the end of the game is anybody's guess, but when he looks down at the weapons in his briefcase, it calls into question whether the Smith Syndicate ever really existed, or whether it was a figment of Garcian's mind? Hmm, but how could that be? Fuck if I know...fuck if ANYONE knows...
Anyway, what a great game, huh?! Definitely one of my favourites, and I had to play the shitty PS2 version. Regardless, the ending was indeed really sad and moving even though I knew nothing about anything, and for any form of media to achieve that, it is truly something.
And I would call it more of an 'art game' although experimental fits nicely too. Yes. More.