This is not doomed from the start, but there isn't enough here yet. Okay, so I agree with Portalmaster8 up there, why does it need to be humanoid? I have ideas of why, but give me a second…
So, with all you have now, this wouldn't be much of an article. Here are some ideas I think could be worth pursuing in order to make this work. Firstly, obviously, where are they being taken? And what does the transition process look like? Of all the D-Class that they have used for testing this effect, have any appeared ever again? Can they send someone in with a video camera and such on the (some sort of rig that works with the effects to get video feed), or does it just transport organic matter, not clothes or anything else?
A major pointer: if there are no hints, like, none at all, to where these things are being taken, this article won't be interesting (or at least, I highly doubt it). So, another way to get some information on where they are being taken: if this is an AI (to be technical, AI's are not physical, so you probably mean a robot with an AI, but I digress), then maybe they can find it's "code". Basically, what if they hacked into its brain and read what the code looked like? This would require some knowledge of coding (or outside help, I know a guy), but could be effectively creepy.
<if $organic=1> trnsprt, $organic = darkhse </if>
That is not real coding, but you get the gist. Hide some creepy implications in the code. On the other hand, if it's humanoid, can it talk? Has it ever spoken and told us anything? Or is it completely silent? Also, what is it's purpose? The answer to this really depends on where they're being transported. Let's take one possibility: it's mind. Say it is transporting things not into normal cyberspace, but into it's own cyberspace. Maybe it was a person. Maybe this is what is left of it's brain. In this implication, its purpose is to be understood, or it has no purpose and this happens on accident because of its situation. If it weren't humanoid, transporting things into its cyberspace might be a way to "contain life" on, say, an inorganic palette. Maybe (although this is very similar to SOMA, and I'm sure has been done in an SCP before), just maybe, it's an ARK. It is trying to contain organic material, because it is trying to transform animals and plants into code. Either it is unfinished, broken, or we haven't found out how to tell it to release them yet.
Another route you can go down (although it would be more of a side thing) is where we found it, but I have no ideas. Figure that out for yourself, also figure out whether it's important to the story or not. You have a lot to work with here, but I'm just gonna say that that goes for most ideas. No matter how bland an idea, you can find things to do with it. This wasn't a bland idea, by the way. Reply and tell me some answers to these questions; I think if played right this could be very cool.
Also, you are welcome to have ideas that aren't mine, I mean, this was just a rant of what I think I could do with it. Every creative mind has different visions and passions. Figure out what you find most interesting.