I need a villain/antagonist

I'm writing a story that revolves around people with subtle superpowers, a private investigator protagonist and something to do with kidnapping (will make sense later). The story is still pretty vague and I'm still working on the physics of it. (Usually, before I write a story, I have to get the fundamentals of the world down.
I cannot think of an antagonist group/organization to go in my story which hasn't got something to do with "Secret government experimentation" or "DNA stealers" or the generic "evil" organization plot. I need something different. Here are the points to consider:

• The world of the story is like our own except there are subtle abilities. These abilities could range from having a really strong tolerance of spicy food to having a photographic memory/ability to create deja vu. (I'm thinking these abilities could come from a gene everyone has and there are certain nucleotides that create them. Longer the sequence of nucleotides, stronger the ability)
• However, I could leave the origin of the abilities are secret and could add that as a motivation for the plot… and the villain…
• I don't know whether the public of the world should know about the abilities or not. It could a) be a big secret and later revealed, the less "powered" people could start creating prejudice. b) everyone knows but it's not been categorized as abilities. People know that some people have a great tolerance of spicy food or have the ability to always creep upon them, they just don't know it's because of "superpowers" nor do they know about the more obvious ones c) Everyone knows about the abilities, they've been categorized as abilities and the prejudice could already exist.
• There are about 9 main characters. Therefore it would make sense for the villain to be a group or of multiple aliases.
• I need this antagonist to somehow incorporate the need to kidnap people as that's a strong part of the plot. I know a father comes to the private investigator to help find his daughter and on this case, the PI finds an escaped "kidnapee"

• How would you react in a world where some people are more "heightened" than others? Would you be jealous? Outraged? Or accepting? What if you didn't have any of these abilities? Do you think extremist groups would be formed in retaliation?

• All the points listed are for context and assistance for the creation of an antagonist

Hello, friend!
It appears to me that you already have a solid idea for an intriguing story and world. This is definitely something I would read, if it were a series or novel. In fact, it has a few similarities to one of my universes that I've been crafting (but don't worry; both of our universes are still very distinct and unique).
I love characters, and creating a good villain is something you'll definitely want to take the time to meticulously craft. I can see you've already put a lot of work into this, and I believe you'll make a killer villain to fit into this amazing world of yours!
Feel free to use my suggestion(s) as you please, but here's my two cents worth.

What if, perhaps, the villain views these "heightened" people as superior to the average joe? If prejudice already exists, maybe he could feel threatened by it. Maybe he has heightened powers and prejudice was shown towards him as a youth (giving readers a reason to sympathize with him, since you always want readers to sympathize with a villain, even if he's evil). The villain could believe that these heightened people are the future, and he is kidnapping them in order to "protect" them from the prejudiced population and dangers of being judged. Maybe he's locking them up against their will, and, despite their arguments, he thinks that he is helping them. This is for their own good.
Of course, he in this context could refer to a group. Maybe it's a small cult-like organization that wishes to make the heightened race superior to the more inferior, powerless humans. But, in the eyes of your villain, the end justifies the means, and he may cross some moral lines to get to where he pleases. Your heroes will see that this man believes himself to be in the right and realize that he is incredibly dangerous both to heightened and non-heightened people, and have to stop him.
This plot can be altered in any way to make a pretty intriguing story. You could cram it all into a single novel or span it out over a trilogy or even a short series.

I love the idea of the private investigator protagonist and the ideas you already have in place. Again— no matter what plot you use, this sounds like a story I would read happily.

Good luck!

This is one of the most professional replies and in-depth assists I've ever had! you certainly live up to your username!
I had never thought of the idea that the villain would kidnap/be motivated in their deeds in order to protect the heightened people, for some odd reason, that circumstance never crossed my mind and I was very focused on them being against these heightened abilities. However, it would make complete sense and is definitely a motive I will keep in mind!
I'm also very glad you are intrigued and enjoy the idea of this world as I thought it would be too generic and put people off (as we currently have a lot of sci-fi and superhero-ish medias out there currently)
I will certainly deliberate on your ideas further and perhaps reply soon with some new details.
You've been extremely helpful! Cheers!