Originally, "Red Museum" was supposed to be a crossover with Picket Fences, a pretty awesome CBS show. However, CBS nixed the crossover after the scripts were written, leaving "Red Museum," an episode which is unfocused and unsatisfying. The lesson: communicate better.
The episode begins with teenagers disappearing and reappearing with words scrawled upon their backs. As the cold open indicates, there's someone looking through a small hole inside one of the resident's house, but that thread dissolves into nothing. The Church of the Red Museum, too, starts off as a prominent force, but nothing comes of it. In the end, it becomes a mythology episode, tying "The Erlenmeyer Flask" to the episode with the Crew Cut Man coming in and cleaning up, likely because the crossover would not happen. Scully's final voiceover tries to tie everything together, but amounts to nothing more than a simple "We know nothing."
Compared to other lackluster monster-of-the-week episodes, "Red Museum" has great ideas behind it from cattle injections to the reintroduction of Purity Control. Unfortunately, the episode isn't very coherent.