I'm answering Fox's question from the reboot premiere: "Why?!"

I believe they are going to connect this season to the mythology they focused on in the first X-Files movie which does fall in line with the series' arc. The mythology basis for my theory is concrete and extensive in the movie. Here's a breakdown of info from the movie necessary to my theory, and I'm using my own twist on a popular "sheeple" metaphor here: The aliens are the "Shepherds" and they're malevolent; human conspirators in high places such as The Smoking Man (TSM), are their "Collies"; and we're the "Sheep". The alien Shepherds have a death grip over mankind- using human "Collies", people in the highest up of places, to oversee their operations on earth. Shepherds were here long ago (H-bomb introduction theory is a smokescreen) and bailed before the ice age but will be returning in numbers. It's implied that the Collies do have ongoing contact with the Shepherds; and their job is to run operations on earth until that point when the Shepherd's are able to return and/or repopulate with greater numbers. The movie features a conversation between TSM and some fellow Collies regarding mutiny against the Shepherds, knowing loyalty meant eventual complete human enslavement/extinction. I believe this "why" question at the heart of the reboot premiere (and all X-Files) mythology goes back to those scenes in the first movie between all the major Collies, specifically TSM.

My theory is that TSM is actually the HERO of the show: preparing humanity to make a grand assault against the Shepherds when they return to use us as slaves and human fetuses to repopulate their species on earth. This Shepherd driven human enslavement/reproduction plan was the plot of the aforementioned first movie and those reproduction plans were already in motion at that time. I believe Collies overseeing this program and knowing its implications is what led TSM to make his ultimate decision to lead a mutiny. So now TSM's been prepping all these years- smoking and ensuring the human advancement of reverse-engineered Shepherd technology 24/7 in order to carry out the most altruistic plan in the history of mankind: a military defense against the Shepherds when they return. Let's not forget TSM has had the means of the entire Military Industrial Complex (including Shepherd tech) at his fingertips- he's the man on earth most capable of saving the species.

Now let's connect the dots: TSM NEEDS to keep Mulder, his bastard son, quiet in order to first to be a good Collie but eventually to save the human race. I'm not certain chronologically exactly when TSM might have decided to mutiny (I believe during the time of the first movie so relatively late) but he logically has equally strong incentive to keep Mulder quiet under both scenarios, loyal to vs. mutinying against the Shepherds. He doesn't have the heart to kill him, bastard son thing and all, so he creates this bogus excuse about not making Mulder a martyr when confronted by his Collie colleagues about it. We know TSM created the X-Files division as his modus operandi for controlling Mulder to keep him spinning in circles and appoints FBI Assistant Director Walter Skinner to oversee the division as his puppet. This Shepherd/Collie/Sheep theme of the Collie rising up against his Shepherd is so pervasive that what results is an X-Files hierarchy in which TSM is the Shepherd, Skinner is his Collie, and Mulder is the Sheep. Skinner does eventually rise up against TSM, forcing him to manipulate Mulder from the outside and making the whole thing an even bigger hassle for him, but he can't kill his son.

Why did TSM say the X-Files being re-opened was a problem at the end of the reboot premiere? If Mulder breaks hard proof of the occult to the public (the man on earth most capable of doing so) then TSM's means to mount a military defense to save us would be highly compromised. Remember, he's taken it upon himself to keep Mulder silent by his own soft methods, all the while facing disapproval from his associates. Doesn't the poor guy have enough on his plate already? He's preparing to save the species using reverse engineered, further Collie advanced Shepherd technology.

So "WHY" Fox?...

Because your father never had the heart to kill you; let's see if that changes as you try your best to muck up his plan to save the species. That's why.

Now as for Tad O'Malley- is he working for the public(altruism and highly unlikely), The Smoking Man, or some other unknown entity? And did he (I believe he did) tamper with Scully and/or teenage latino abductee's(forgot her name sorry) blood/results to get into Scully's and therefore Mulder's head?