As a weird comparison, How I met Your Mother did a good job with this. I don't blame X-Files for not having a plan necessarily when pitching it, and I get that TV is complicated because who knows if you'll be picked up, make it past one season, or how many you'll go for. But, HIMYM planned for that in giving the show "offramps" depending on how long it went, and it's pretty clear with the series length.
If cancelled at Season 1, Ted would have just ended up with Robin. Hooray, people feel good.
If cancelled at Season 3, Ted would have ended up with Stella. Hooray, people feel good.
If cancelled at Season 6, Ted would have ended up with Zoey probably. Least favorite but they were clearly building her up as a "just in case".
Then they brought in Tracy for Season 8-9.
You don't need to know every detail, but you need to have a general path for your show, and X-Files... did not do that. It just kept meandering. The worst was that it kept adding more plot to the story, more stories, but then for writers you have to maintain those stories and that plot. You have to remember what happened to not contradict yourselves, and the only way to easily get around that is to.... add even zanier things. It just went off the rails.