Oh they definitely end up making it up as they went along and contradicting themselves, but still it feels like viewers often dismiss the mytharc episodes completely because of that, making out that the MotW episodes are the only ones worth watching. But really the mytharc episodes had their moments as well, especially when it came to deepening the characters of Mulder and Scully. I can't imagine seasons 2 and 3 being half as memorable without some of those two-parters