Worse than the Antagonist
Question: Suppose that the protagonist starts out as the good guy pursuing a moral goal and the antagonist is the villain that is in the reconsider role.
But what happens if over the story the protagonist eventually throws off his hero persona and tramples on it, in the process becoming several times worse than the antagonist.
How does this change the relationship between these two people, and how would that be perceived by a reader?Response:
First, you have to consider what message you want to deliver with your story. You can think of a story as an exploration of whether a particular approach to dealing with a particular type of problem will lead to a good or bad ending.
Traditionally, if the main character chooses to become immoral, he suffers unhappy consequences. In addition, if the Story Goal is not achieved, because of the main character's choice, the world suffers the Consequence. We call this type of story a tragedy.
In the scenario you suggest, if the main character, because he changes, fails to achieve the Story Goal, we would expect a bad judgment for him. He would end up in a worse state than at the start of the story.
It is possible to have him end up in a better state - a judgment of "good" - but then you would be giving the message that immorality is the better choice.
The main character might end up allies or friends with the antagonist - or perhaps just stuck with him because the rest of the characters shun them both - but the world will still suffer and, I suspect, the pair of them would appear despicable to the reader.
So what it comes down to is the message you want to deliver. Do you want to argue that "crime pays," or that "morals are for fools"?
I'm guessing not, especially because that will not sit well with most readers. So that means you are probably writing a tragedy. Even if the antagonist is happy about his triumph, the main character is going to end up miserable and regret his decision.