This is the story on the return so far.
For years, the execs at Fox were not very Xfiles friendly (despite some MAJOR efforts from the fan communities i.e. twitter trending campains, sending 1013 pictures to the people at Fox, etc) after the original run of the show. In the last year or two, they stepped down and the people running the network are the folks that were producers of all the sucessful programming that Fox had in the 90s.
About 1.5 yrs ago, rumours of a BluRay restoration of the show were in place. Then some proof started to surface and people started to speculate something was going on beyond a simple release. Now This effort was something fans had never seen before which started the speculation, although it was clear to fans that the Xfiles fan base in the past 8-10 years had actually GROWN, thanks to the reach of the internet and netflix. Many fans were always left wondering why Fox didnt really understand this cult following.
Now Chris Carter, GA, DD, Spotnitz, etc. have all been game to return at any given time during the years. The problem was always the heads of the network who did not believe the show could perform specially after the response to t he second movie (why those same exec guys thought it was a good idea to put it against TDK is beyond me). The network was the reason. Not the fans or the talent in the show.
Now time has passed and everyone was busy, but at some point Carter and Fox started having conversations about the show. Its obvious that in a landscape of mythology and world building that is tv and movies now, the xfiles was a pioneer and a crown jewel as a franchise. Not to mention they fully own the rights to the whole thing. Make no mistake about this, Fox spent big on the marketing of the show like it was exctly that: A major franchise. It came through big. They own the property and would clearly like to milk it from a business perspective.
This is why you are seeing an established logo, merchandise, new characters and a cliffhanger ending. No doubt that the idea is to return and it will happen. This even series sets up a whole story arc moving forward. The idea was to continue and I am suspecting Carter and Fox have a roadmap including perhaps a theatrical release. Theyve gone even as far as to hint that they will make more to flat out say they want to or to for example call the end of the event series a SEASON finale. No reason to think everyone wont make the effort to keep it going. Now this whole were too busy cant do full seasons is a legitimate concern with GA and DD, but I think its also a negotiation tactic. I believe they will become available in time once Aquarius is out of the equation and Miller and Einstein are there so that they dont have to carry so many hours of taping by themselves.