The only concrete piece of info I have about this upcoming story arc -- it involves aliens having infiltrated the Trump administration.
Chris Carter isn't really involved in the comics. For the comic book SEASON 10, Carter consulted on the first five issues. Writer Joe Harris wanted the villain of SEASON 10 to be a teenaged William with telekinetic and psychic powers, taking control of the Colonists and Rebels with a new faction called the Believers. But Carter vetoed this, saying he wanted William saved for THE X-FILES III if it ever happened.
Carter also provided some guidance so that Harris could steer clear of any plots that would contradict a future feature film finale. But we got a TV series instead, Carter had a different vision for THE X-FILES on TV and the comics became part of an alternate universe that wrapped up (somewhat abruptly) before the comics shifted to the Revival universe (with the same writer). While Carter's name is on the covers and he has an Executive Producer credit and he reads the comic scripts, he's not driving it creatively.
Anyway. Joe Harris and I are of very similar mindsets politically and creatively -- his X-FILES comics are essentially the X-FILES version of SLIDERS REBORN (obsessive love letters to the legacy and history of an unfinished TV show), right to the point of using the same title in our stories where icons of 90s sci-fi TV take on Donald Trump.
So, keeping with that, I imagine a situation where Mulder's old friend, Senator Matheson, recruits Mulder and Scully to investigate potential sleeper agents in the White House administration. It's revealed that the sleepers are actually the fire aliens introduced in THE X-FILES #1 (2017) that have been taking over human hosts for some unknown endgame, and Mulder and Scully find themselves forced to protect Trump and his staff from an enemy only they can fight, wrestling with the conflicts between their beliefs and their duty.
Continuing with the conceit that Harris and I think the same, I'd never have the sliders -- or Mulder and Scully -- defeat Donald Trump. In fact, I think it would be critical that Quinn, Mulder and Scully end completely beaten but score some sort of symbolic, moral victory.