This is the third X-Files case of John Doggett's. If you don't think he was pulling his hair out by the roots before this, think again.
It appears that John has the same problem that the kid played by Rodney Eastman (Ronald Purcell) has- neither of them can deal with the fact that a kid named Billy, (Kyle and Ryan Pepi) is even walking around. "Ronald" knows why, but cannot come right out and say it. Because he doesn't believe it, just like Doggett. But for different reasons, Doggett is trying to deal with this case as if it were a normal child abduction case... but it is far from that.
Skully, of course, can blurt it right out. But even she can't come to grips with what this case represents. She has not seen anything like this either, so she is also woefully unprepared. This is a conundrum that Billy's mother, Kim Greist from "Manhunter" and "Brazil" cannot face either. Speaking of "Conundrum", the father, played by Erich Anderson, was in the Star Trek: next generation episode of that title as "Cmdr Kieran MacDuff". So the entire cast was pretty well selected, solid background in the supernatural or weird.
The main purpose of this episode appears to be to drive Doggett bugsputz. It was also a good way to introduce his past working child abduction cases- he gives the impression that he has had a lot of experience, but this is far beyond his expertise.
Rodney Eastman appeared a couple of years previously in a 1st season episode of Chris Carter's other show Millennium, where he plays an "angel" named Sammael. As he had aged a bit since then, he was still able to portray a younger version of himself as well as the older version that Doggett deals with. But he plays this kid basically the same way as he played the angel, with a tight lip.
Nothing is really explained, I think this was mostly provided to get us to think about what happened and why. And to give Doggett something really intense to chew on. Remember, Doggett is the guy that when presented with evidence that says a certain thing happened, even when he sees it right in front of his face, he simply cannot believe it. And because of this, he cannot ask the "Ronald" character the right questions: because Ronald does not believe it either: they are both alike in this regard.
One final thing that we can dredge out of this episode is that Ronald knew what had happened, although he could not talk about it, or name his mother's boyfriend "Cal"- (Jim Cody Williams- who ironically is going to be in the first episode of season 4 of Westworld. I had never looked up his filmography, he's had a lot of great parts, even in Traffic (2000), and a stuntee in ID4). There is a lot of untold history between Ronald and Cal. The fact that they don't mention any of it, gives us more to think about.
It's the part of the story that is not said, that gives us most of the answers that we are looking for.