I have the principal antagonist for my modern fantasy alternate world setting. Unlike the typical antagonist, this particular character, whom I named Vritra. He weilds the exaltation of a goddess, which granted him a slow aging, stronger than average magical capabilities and fast healing far beyond what the main characters can access. He used to be a very respected member of the magic association, and once destroyed the incarnation of a chaos god, saving thousands of lives, however he was deeply contaminated by chaos.
Short time after that he found out how that particular incident was because the neglect and corruption from the magic association. He also found that the only way available under the circumstances to prevent more incidents like that one would end up cutting the ties that the people had with magic, however the association wasn't particularly happy about it. When he tried to bring the issue to the public, the association labeled him as a traitor, and conspirator and tried to kill him.
From then and onward he fought alone, externally against the bounty hunters from the magic association and against the forces that threatened the world (which the mage's guild were neglecting, for fear of loosing their monopoly on the magic and overestimating their ability to solve the issue without giving up on the magic). And internally against the chaos that was corrupting his essence. After several years he has come close to finally cutting the ties to the mana, but has become so corrupted that he's loosing his sanity. He kills not only to defend himself but also for pleasure, and since long ago stoped caring about the consequences of his deeds, no matter how high the price, he will accept it in order to accomplish his objective.
My problems comes in his impact to the plot. I fear that he might be bordering on marty stu territories. He is not the strongest mage, nor he has a particularly wide array of spells to use, but the few he has are versatile and strong. So far he has meteor swarm (deadly, and can be spammed to some degree); a limited, non spammable flashstep, that he uses to cut distances and blast someone pointblank; a strong chaos emanation (the one that gives me headaches) that easily disrupts mana, breaks spells and deals severe damage to magic casters, but using it propagates his own corruption; strong, telepathically controlled fire chains (but require him to focus on controlling) and a partial dragon transformation that puts him near the level of the stronger physical fighters, but limits his spell to fire and lightning blast. He is also skilled in close combat, posses a great magical resistance, and on his more sane moments is a great tactician (but easily gets carried away when he's exited in a fight)
So far I use his corruption to limit him, even tho the exaltation grants fast healing and a demigod stamina, the mental straint of containing the chaos limits how long he can fight, also all of his spell requiere huge amounts of mana and can't be cast together lest he risk loosing control of the chaos.
I also had him loose one of his dragon wings at the end of book 1 (cutting his sky superiority, for flying here is rare and unique), and during book 2 he sustains severe wounds fighting a demigod while off camera that impair for the remaining of the series, but also gained a manadrain spell that gave him a huge edge on a fight that would have killed him before the climax (and somewhat solved the issue of his spells requiring huge amounts of mana).
What else could I do to limit him? or are the limitations imposed on him fair enough. He's supposed to win in the end, accomplishing his objective of cutting everyone's ties with the magic, causing a global catastrophe, but ultimately saving the planet, but he also has to die just after that, in a post climax fight against the protagonist (that ends just as they are loosing their cuts to the mana). I have already planned the climax, but I feel that he needed a bit of deus ex machina to get there alive, and I want his victory to feel real, not just because I, the writer, said so
P.D.: He is the "protagonist" of the global story, my main character is the protagonist of her personal story, and serves to narrate Vritra's story (besides a few, particular chapters, I don't want to have him as the narrator, mainly for the Marty Stu issues, and mainly for I want to make the point that the story resolves around a LOT more characters than just the protagonist)