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I think you misunderstand what Protagonist-Centred Morality is. It's not just that the narrative "encourages the audience to root for the protagonist despite the immoral and unethical actions". You...
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#4: Attribution notice removed
Source: https://writers.stackexchange.com/a/39285 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#3: Attribution notice added
Source: https://writers.stackexchange.com/a/39285 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#2: Initial revision
I think you misunderstand what Protagonist-Centred Morality is. It's not just that the narrative "encourages the audience to root for the protagonist despite the immoral and unethical actions". You get Protagonist-Centred Morality when the whole narrative's moral compass appears to point not north, but wherever the protagonist is facing. Whatever the protagonist wants - it's right for them to want it. It's not OK to hurt the MC, but it is perfectly OK to kill by the dozen people whom the MC doesn't know. If the MC does something bad, there's an excuse for it, it should be understood and forgiven, but when somebody else does the same, it's irredeemably evil. To avoid this, you show that bad actions are bad, regardless of who does them, and towards whom. The protagonist's bad actions don't get "understood" or "excused" just because he's the protagonist. Since you say your protagonist gets called out on his bad actions, I'd say you're on the right track, Protagonist-Centred Morality is not a trope you need to fear. As for the protagonist being a saint compared to the antagonist, that's a separate issue, and is a problem with the antagonist. An antagonist who's all one-dimensional evil is boring. He too needs to be faceted, nuanced. In fact, since your protagonist is very flawed, but eventually chooses the hard path of redemption, it could be interesting to make the antagonist face a similar choice, and pick the dark path. He could be a dark reflection of the protagonist, his choices condemning him. Regardless, the reason to root for the protagonist should be contained in the protagonist, not "because the antagonist is worse". That path leads easily into [Darkness-Induced Audience Apathy](https://tvtropes.org/pmwiki/pmwiki.php/Main/DarknessInducedAudienceApathy). Find a light within your protagonist, a reason for the audience to wish for him to pick Light over Darkness. Show us that there is something within your protagonist that's worth saving. Then we'll root for him for his own sake.