Chris Carter didn't get that far in his hopes of turning this into a film franchise, as Fox decided to renew the show and hold him in for at least another season. This is also a franchise that works way better on television as the first feature film proved, so this was probably always the right move. But that doesn't mean that they have to abandon the film ideas, and it's clear that Carter wanted it all to feel interconnected. This episode does a lot of work paying off what was done in the season five finale, but it fails to properly address the film.
It is not beholden to what happened in the film, but it would have been nice with a little bit of ramifications from the events of it. By the end, it felt like Scully had turned a corner in terms of believing in Mulder's claims of extraterrestrial life, but the show finds her right back in her doubt corner. It continues to be a wonder that the writers keep putting her back there and claiming her doubt as she has been through quite a lot at this point, even if being kidnapped by aliens wasn't enough already. However, the opener does take its time to follow up on the things that it began in the fifth season finale, and a lot of that overflow makes for quite compelling television. The arc of Gibson Praise is still not done, and he continues to be a very sympathetic character, especially seeing the treatment he faces under the Syndicate. How he fits into the larger narrative is also expanded here and it's an interesting direction to go in, although it feels like it could potentially end up in a very uncomfortable corner if it's not done right. Carter also throws an unexpected twist into the mix concerning the X-Files and its leadership and that may turn out to be the most interesting factor of this premiere, and it certainly creates a new dynamic between the characters, which I'm very interesting to see extent into the remainder of the season, unless they decide to cap it, which would be very disappointing.
"The Beginning" does feel like a new beginning, but it probably should have done a bit more in terms of closing all the unclosed doors. However, the storylines continue to be interesting and the character dynamics gets a very fascinating shake-up that will surely bring a lot of tension to the rest of the season.