Hi there In the story I am writing, there is a twist that reveals a side character to be the main bad guy. Before that point, he is like a bumbling, gentle uncle. I should say that his motivation is admirable, he genuinely believes he is doing the right thing, and that the ends justifies the means. How can I make him a credible threat, but also a credible character? I mean, he has to be a very real problem for the protagonist, but at the same time, I don't want it to feel forced, as if he could simply be talked out of his position.
If you have this side antagonist show great loyalty or at least admiration for the cause of the main antagonist then it will be believable that he'd stick to his ideals when the main conflict comes into play. Even if people are bumbling and gentile they can still have the moral fiber to stick to what they believe in. What you have to do is make the reasons why this character believes in the main antagonist feel true and understandable from his point of view. It will probably require some back-story as to why what is doing is the right thing in his mind. If this character is also being manipulated by the main antagonist, and that manipulation is shown to the reader but not the character, that will also help identify with him. It is easy to understand why the rich landholder uncle wants to side with the evil vizier, because his plan has strength and stability for all the people of the land (as far as the landholder knows). It's understandable that his young orphaned niece would run into conflict with her uncle as she tries to run way with the leader of the rebels to overthrow the evil dictator. The uncle may like the viziers plan because subjugation is a less violent means, where rebellion leads to outright war and massive instability. This tension in that character between his choices is an internal conflict that can drive the story forward on it's own, in addition to providing a more literal challenge for your protagonist to overcome. Having that character deal with the ramifications of his choices will also make him more human and understandable. It will feel forced if this character comes out of nowhere just to add plot element and another conflict, then leaves the story. At that point you can see that he's just a mechanic to draw the story out, and not truly part of it. Good luck
Without having read the story, I can only make abstract suggestions, but I'll do my best. Drop hints throughout the story to indicate this uncle is a threat. These can be subtle, but when the readers think back, they would go, "Oh, of course!" AlexSivier, I've noticed that you have Kyoto, Japan set as your location. It's cool to have members from across the globe here! I visited Kyoto late last year. It's a beautiful place.
Okay, going to draw some inspiration from one of my favorite novels, Vampire Academy by Richelle Mead. She has kind of the same exact situation, bumbling uncle and all actually, who turns on the two MCs and actually tries to harm one of them while dispatching the other while he did so. He believed in going through with his plan no matter the consquence, and even did some drastic things to prove it! To me, I think making this uncle character someone the MC actually might be afraid of is one way to go. Another way is to have a change in the uncle so that it shows his decision to follow through with what he believes is right is cemented, and he's not going to be able to be talked out of it, as you say. Foreshadowing, as marcuslam said, can also be a great, great tool! I don't always pick up on it right away as a reader, but once it comes to a conflict/climax, I slap my forehead and go 'Duh, of course that was going to happen!' I'm not sure if I've hit on what you've asked me to, but I hope I helped in some way!
You mentioned his motivations and desires. Concentrate on those things and let the readers see his reasons even if they don't sympathize with him.
I'm going through the same thing right now with my current write, except the antagonist is just deceiving others with his gentle and nice behavior. I'm not sure how I can help, since I'm struggling myself, but the others already summed it up. It's really important for this character to have good motivations to be on either side at the given time. He was nice, why? What made him side with your protagonist? He became the enemy later, why? What made him turn against them? Although if you want him to be a threat then he should have great attachment to what he's doing, it should be something he'll give his all for and not hesitate for any decision. Like the greater good or something.
When you say this are you referring to his motivation being admirable to him or in general? There's a difference. What really matters is the way you present his motivations, desires, interests, etc within the context of the story. His actions and words will justify his behavior and the resulting conflict will ensure a good read. Conflicting feelings about a character or story can be powerful to an audience.
One thing I do is try to understand people I disagree with. In real life, there aren't really good guys and bad guys, most people have admirable motivations, and yet we have vehement disagreements which are hard or impossible to resolve. Take the abortion debate for an example. On one side, you have someone who truly considers an embryo to be a full human, morally equivalent to a (born) baby. Killing the embryo, no matter how practical it is, is just plain murder. They'll react in much the same way as they would to you suggesting that killing a newborn baby is a good idea for various practical reasons. (And given how common infanticide was and still is, it's clear that there are practical reasons for killing newborns, often the exact same reasons that people have abortions.) On the other side, you have someone with strong empathy for the plight of a woman with an unplanned pregnancy. They don't consider an embryo to be a human being yet, just a bundle of cells, and this bundle of cells has the potential to ruin the woman's life - or maybe even kill her. To them, it might seem like if someone argued that you shouldn't have chemotherapy because the cancer cells are living human cells and are deserving of protection. Both people are basically good people, with basically admirable motivations, but do you really expect them to come to an agreement and stop fighting each other?
A winning smile and kind eyes have blinded many people. If the uncle is able to pull of the innocent, happy-go-lucky persona most of the time all the read has to see is that sometimes there is an evil twin under what everyone sees.