Let’s start with the ending of the second season, which is much more of a clear cliffhanger than the first season had. Mulder is seemingly dead after entering a cache with the remains of aliens, which soon afterwards is destroyed by the Smoking Man and his goons. Cut to “To Be Continued”. What the cliffhanger implies is that the show’s creators were much more sure of its continuation than at the end of the first season (or much more desperate). Anyway, for a big season finale, everything looked kinda cheap. TV-series sure have come a long way in recent years.
While X-Files is one of the first shows that people remember where seasonal arcs or the entire show arc became more prominent than single episodes, thats not how it feels when watching the show at the ground level, at least in the second season. Sure, the elements of the superarc are always prevalent, from start to finish. The X-Files are closed, at the start of the series and Mulder and Scully work in different departments.
For a few episodes the X-Files remain closed and Mulder is working dull routine stuff (transcribing tapes) and is occasionally sent to help with strange cases (where Scully helps from afar). Then, when Scully is abducted for two episodes (mostly due to her actress being pregnant), Mulder’s superior Skinner reopens the X-Files. Later things get even more complicated with more layers to the alien conspiracy (clones, different alien factions, etc.), but despite all that, the single, non-conspiracy episodes remain relevant.
Relevant in the sense of keeping the show interesting, offering variety and a counter-point to the whole alien conspiracy superarc. Not every single episode works and some of them are downright awful, but they together with the superarc are what keeps me watching. I like the superarc, but that alone would get boring fast. Mixed with all the other stuff: nearly mundane cases, the monster episodes or the truly weird ones is what keeps the series fresh.