Btukfyl

My good guys murder people. They slowly carve runes onto them to help defeat the bad guys. Sure they try to use "society's worst" people for the rituals, but realistically that doesn't always happen.

This is revealed to the main character and when the MC pushes, the good guys are unapologetic about all of it (similar to how the first paragraph is written). Of course MC shuns them and dissociates himself with them.

My goal is to make the MC come to view the good guys as Good Guys.

Eventually, MC realizes that the killing is necessary and comes to accept the good guys. But I can't get him to go from accepting what they're doing as necessary to then believing they're Good Guys. How can I make this leap? What am I missing?

Edit: In response to a comment, I'm not asking a "what to write" or what my plot should be or how the world should work. Rather, I'm trying to make a character pull a full 180 on their perspective of "right" and "wrong" or what is "good." I've begun the turn and am (what I feel to be) about halfway--my MC has accepted what's happening as necessary but still feels uneasy about it. I'm asking about how I can push a character over the edge and twist their beliefs while making it more believable than "He woke up the next day thinking they were good." What should I focus on to make this believable? At the moment, I feel like anything I do will be clearly fake.

According to Adam Smith's The Theory of Moral Sentiments, proper moral sentiments may be defined as how a disinterested observer would think someone ELSE ought to feel in a given circumstance. Given that yardstick, I am not myself convinced that your MC is wrong. My own reaction is that anyone who isn't horrified by committing brutally cruel murder is morally deformed - no matter how important it happens to be for that specific carnage to continue.

It sounds as if your character's moral compass is functioning correctly.

Organic characters don't always feel or act as the author intends. In the case that your characters grow organically, you have to negotiate with the character, and accept that you can't always steamroll them into occupying exactly the place the plot called for them to occupy at a particular point in the plot's progression.

How can I make this leap?

The MC needs proof he cannot deny. Perhaps, by his own hand, he doesn't just shun them, he takes action to prevent this ritualistic murder from happening. What are the consequences of that?

There better be some consequences, or these ritual murders are not accomplishing a damn thing!

But there are consequences, weird consequences that cause extreme pain or even death to innocents, perhaps to children. And the weirdest thing about these consequences are that they are precisely what the "good guys" told the MC would happen; and they are too magical or weird for the good guys to have done this harm themselves.

In short, the MC believes this is proof the good guys were right. Once he knows that, he can still try to squirm and see if there is any other way to prevent the consequences without having to commit torture and murder. Perhaps that is part of the plot, him trying and failing to find an alternative (or eventually trying and succeeding).

But the turning point is accomplished; at this point the MC has left his "normal world" and believes the good guys are on balance doing good, and he needs to join them. How long all of this takes depends on whether you have a bigger plot in mind. Just the conversion of the MC could be a story, but it could also be a short intro into a larger story if he has a bigger problem than this to solve.

Edit: All that already happened...

The question was how to move the MC from seeing the killings as necessary, into participating in the killings.

But the answer is the same, it is still by showing the consequences of NOT killing. He thinks it is necessary? Then invent a reason that makes him the only one that can do it. One or more of the good guys dies, or gets incarcerated or otherwise taken out of the picture, so there isn't enough of them to safely capture and kill a criminal.

Your MC has to step in, or the consequences kick in. Force an emergency on him. If he truly believes the killings are necessary, he will blame himself for whatever innocents suffer if he doesn't step up when he is needed.