To give some background: In addition to human realm there are multiple other realms that are connected to it. The races that occupy these realms are the basis of many of our mythological creatures and lore. Magic does exist, but is more likely to take the form of artifacts that perform certain functions vs fireballs, or shapeshifting. Many of the realms do not get along/are actively at war. Many of the realms are active on Earth as we are the nexus between the realms. Humans as a whole are not aware of magic or the other realms. We have a human organization that knows about the other realms and is working to deal with some of their nastier elements here on earth. A human reporter has recently found out about the organization, but thinks they are a mass murdering cults. He is now trying to do an undercover investigation. The organization has become aware of his investigation. I see 3 main ways for them to react: 1. Kill him. 2. Bring him into the fold. 3. Discredit him . #1: Upside: He's completely out of the picture, risk eliminated. Downsides: Killing someone who is part of the group you are suppose to be protecting. Risk drawing police attention. Risk attention of his colleagues if they knew he was investigating something. #2: Upside: If he is brought into the fold, he's not as likely to talk. Downsides: If he's not really loyal, he now has access to more damaging info. #3: Upside: He's not dead, if he does report facts, less likely to be believed. Downsides: Alive but likely to have a vendetta. Any other options that I missed, or potential upsides/downsides? For option #3, how would you discredit a reporter well at the same time eliminating any threat of him sharing any of the information he does have?
As far as killing him... disappearances happen a lot in real life. If they make it look like he packed and left, then there's room for skeptics to assume he's fine. What about black mail? The reporter could have some closet skeletons, or perhaps a loved one that need be threatened. They could frame him, too. It sounds like their work generates a lot of bodies, and they have influence and power. Dump a few stiffies in his apartment and call in an anonymous tip. Later, if they still want to finish him off, they can just Epstein him. Edit: because I'm dumb.
You should think through the real conundrum here, which is to decide which is more important to the group—maintaining their secrecy or protecting all humans. In fact that question should come up for the group in the story itself, since it came up so prominently in your development. They could argue about it for some time. Another option would be to trap him in a faraway realm where he can live but can't get back. Maybe they could check on him from time to time, make sure he's ok or even set him up to live comfortably like a posh prison. Possibly they could even let him return form time to time on a probation basis, at those times when the voices of compassion win in the ongoing argument about his fate. They run the risk of his telling abut them, but they can keep an eye on him, or even hold him under some sort of magic restraint. Or you could do the David Banner thing from the 70's Hulk TV show (I think that's the one where they changed his name to David?). He had a nosy reporter that was always snooping into his story, so each time he had an 'incident' in a town he'd hit the road like Kwai Chang Kane from Kung Fu, travel to a new town and start again. But each time the reporter would track him there and he'd have to leave again, like a lone gunslinger in the old West. Might not work so well though for an organization.
The thing about one reporter is there is usually another just waiting to jump in and take the lead. Basically, the reporter's editor(s) would be aware of what this reporter is working on. Dead or goes missing might make the editors believe it's an even bigger story and stick a few more reporters on the assignment or to look into things. And that's just one newspaper or magazine. Can you really keep all the reporters away? Introducing this into your story might be opening a can of worms. It's also pretty hard to discredit a reporter, especially one who has worked their way up to doing undercover and investigative reporting. I also see it highly unlikely that a reporter would ditch their obligation to the news and uncovering truth to team up with your group in any way. Maybe you're group needs to hire a good PR person who can spin things for them and throw reporters of their tracks.
I know this is a bit of a hot mess of a situation, but that was one thing I always found weird about 'The Masquerade' type scenarios- How do you maintain it when everyone has a smartphone and an internet connection? At least some, like the Dresden Files give an explanation-magical beings emit a field that screws with modern tech without them even trying to. Since it was something that always bugged me, I feel like I need to at least make a crack at it. The reporter in question is from a small internet news site(he makes a joke that their twitter feed has 8 followers, 3 are employees, 4 are employees relatives) that mainly does papparazzi style news and clickbait headlines. He stumbled on the group quite by accident. One of the senior members is in favor of killing him and his editor because that is the most sure way of eliminating the risk and allowing the organization to continue with their work(Greater good for the greatest number). The suggestion to bring him over to their side was proposed as an alternative to killing, but they have pretty severe trust issues, and if they let him know more, they risk exposing themselves to more danger. That's why I was looking at the third option: Discrediting him. If it could be done in such a way as to convince the editor that there is no story and make it so no respectable newsite would touch him it could be possible. However, he'll still be alive, and now convinced that he was right, so it is kicking the can down the road. Worst case scenario is he keeps trying and creates his own website to spread the news. Well most people would think he's a crackpot, there are other things than people who would know better.
In Stranger in a Strange Land Heinlein has the nosy reported kidnapped for a weekend, drugged, and left by the side of the road (figuratively) soaked in booze and hooker perfume or some such. Make it look like he's a drunk, womanizer, child molester, something along those lines. Look into the downfall of Chicago Tribune reporter Bob Greene for hints on how things can play out when sexual activity is on the line. On the other hand, you said that "Humans as a whole are not aware of magic or the other realms." One way to discredit him would be to expose him to a whole bunch of information about the other worlds while blocking him from verifying the information. Take him to the Land of Nod or Narnia or whatever, show him the Faerie Princess on her throne, confiscate and destroy all of his recording devices, and turn him loose (hmm, this is going the same way as my first suggestion, sorry) naked in Central Park with a head full of LSD or meth and a cell phone. There on out, if he says it's raining, his editor is going to send an intern outside to check.
Yeah, that's kind of where it's going, plus I realized I had inadvertently wrote myself an out in a previous story set in the same universe- the existence of an artifact that could be used to manipulate someone.
Still working on getting the 'discrediting the reporter' part of the story the way I want it. However, by looking at this and how each of the characters proposes addressing the problem, it has opened up new aspects for future stories. I have decided one of the characters is a specist and well is in favor of brutal actions against non-humans, is against hurting humans. This is going to end up creating a schism as the main founder of the group is more concerned with just limiting the nastier elements. The Specist(or should I call him a Humanist?) only has limited knowledge as the leader is cautious sharing info with other members so most know only certain aspects, and most don't know more than a few of the other members. What really makes the Specist a problem is that one of the primary leaders is not human, so his views bring them into conflict. It's always interesting to see how working on one part of a story can open up avenues you hadn't considered. I had been planning on taking these stories into darker territory and this creates a good avenue for that.