Okay, I'll be that asshole.
Since Mortal Kombat 4.
His status as a zombie demon ghost gets retconned as being a slave of Quan Chi. He is "freed" somehow in a few of the many contradictory endings of MK4 -- he finds out Quan Chi killed his family and ninja clan and not Sub Zero. He then decides to hunt down Quan Chi for revenge instead of Sub Zero, which technically makes him a good guy, in some sense of the word.
Then in Deception he gets stated as being the designated "Champion of the Elder Gods". Basically that he's the guy who's supposed to actually beat the big fuckoff bad guy dragon. Basically yes, by this point Midway tacitly admits that Scorpion is secretly now the main character, because they kill off Liu Kang in Deadly Alliance.
In 9 the timeline resets and he's back to being a slave of Quan Chi, but has misgivings when Raiden says, "You know...maybe being a zombie demon ghost slave of that pale guy isn't a great idea..."
During 10 they defeat Quan Chi and actually give Scorpion his humanity back instead of having him stay a zombie demon. There's a whole scene of him saying "My name is Hanzo Hasashi" even rejecting the idea of being Scorpion.
In retrospect, I feel like this is more indicative of Mortal Kombat's shitty writing than anything else, but Bob was more or less correct in that according to modern Mortal Kombat, Scorpion is a protagonist.