From a screenwriting perspective, this episode starts well but goes downhills near the end after the boy's second abduction. Now, (in TV/film) the protagonist should do their best to overcome an obstacle, "destroy it or be destroyed by it" in order to resolve their inner (pathos) and outer conflicts (action). It should be their decisions that make them succeed or fail. The episode is about Scully, considering that in the closing scene it is her whose inner conflict is resolved when talks to the priest.
However, the screenwriters seem to be unsure of how to end her outer conflict. In the final showdown where Scully is supposed to make a crucial choice the situation just solves itself with the antagonist falling into the shredder and the boy being saved. And meanwhile miracles are the main theme of the episode, here they seem to be confused with deus ex machina. The ending could have been probably much more powerful if Scully made a really bad choice (or a seemingly good choice which turned the situation worse overall) in saving the boy which then could have threatened with imminent failure and then just slightly aided by a miracle. What I just described is actually somewhat there in the showdown scene but not emphasized enough in my opinion, Scully is more of an observer than an active participant, for which it feels anticlimactic to me.
However, the screenwriters seem to be unsure of how to end her outer conflict. In the final showdown where Scully is supposed to make a crucial choice the situation just solves itself with the antagonist falling into the shredder and the boy being saved. And meanwhile miracles are the main theme of the episode, here they seem to be confused with deus ex machina. The ending could have been probably much more powerful if Scully made a really bad choice (or a seemingly good choice which turned the situation worse overall) in saving the boy which then could have threatened with imminent failure and then just slightly aided by a miracle. What I just described is actually somewhat there in the showdown scene but not emphasized enough in my opinion, Scully is more of an observer than an active participant, for which it feels anticlimactic to me.