Alright, let's go piece by piece, because I have several objections to this theory:
From enttry 37, we find out that Alex has been pursued by The Operator since his childhood. After a certain period of time, up to the middle of production of Marble Hornets, Alex is oblivious to what is going on. He soon realizes something is wrong with his life, and begins to film himself to keep track. Several of the entries which we can definitely date as mid or early production go in this time period (I'll get to the later dated entries in a moment). Alex watches them several times over, and for the first time in his life, realizes The Operator is in his life.
Firstly, there is no evidence in enttry 37 that the Operator has been stalking Alex since childhood. The shot of the Operator and the shots of Alex as a child are entirely separate shots edited together; it could just as easily have been TTA/a member of TTA editing the shots together per his usual MO.
Secondly, Alex encounters the Operator even before he starts filming himself; Entry 12 and Entry 2 are indicative of that.
Now, Alex goes from running to pursuing The Operator.
This is a major discrepancy: why? Why does he do this? Where is the evidence that he does this? The only thing we ever see is Alex running from the Operator, and even if we accept your theory as true, there is a notable absence of motivation for him to do that. What makes him go from first noticing the Operator's presence to suddenly pursuing him?
However, it becomes apparent to Alex that The Operator does not simply want an assistant; it wants someone to give its powers to.
Going to hit you with the why again: for what reason? WHY does the Operator want to "give [up] its powers"? Where is the evidence that this is something that was ever happening?
For whatever reason, Alex cannot be given powers
What reason and where's the evidence?
so Alex has to find someone who can be given them. At this time Marble Hornets has reached mid-production. Alex puts up a show for the cameras, acting like he is the victim of The Operator, all the while seeking out for a member of his crew to be given The Operator's powers. Alex is unable to find one, and decides to give The Operator every one on the crew to convert, as if they could not be given the full content of TO's powers, they could still become assistants. However, right off the bat, Alex and The Operator get their man: Tim.
Entry #51 begs to differ; if Tim is the one they wanted to transfer the Operator's powers to (a conjecture that I still don't agree with at all, but for the sake of argument), then why would Alex lure Brian into the school/hospital/whatever thing in entry #51 when it is shown that they already have Tim captured?
But something goes wrong. The conversion process to become Masky does not exactly work as planned. For whatever reason, Tim does not go completely under The Operator's spell.
For whatever reason
And what reason is that? These "for whatever reasons" are massive logical holes in your theory that need evidence to back them up; if you plug those holes your theory as a whole will be much better.
At times he would work for The Operator, not questioning anything, at times he would know and have his powers while not under The Operator, and at times he would be not knowing of anything. Perhaps this was due to the extent of his powers, perhaps he was resisting, perhaps Brian finding him in Entry 51 did something, the answer is not certain. For whatever reason, this happens to Tim. As time goes on, the conversion gets worse and worse, as Tim starts to take the medication seen in Entry 20 in order for him to remember the Operator and his powers while not being "evil". Alex always makes sure to watch Tim, and manages to squash any resistance from Tim in order to convert the whole crew.
Wait, they're back to converting the whole crew again? I thought Tim was their man?
But Alex slips up. Tim finally manages to figure out who and what is behind the scenes and realizes that if he does not do something soon, The OperAlex will win. Realizing Jay has not been converted, over a period of time, Tim does a small version of the power transfer process and gives Jay a small extent of his powers.
This however is enough to distract The Operator and/or Alex from being converted. This however had no effect on the others, and everyone else is converted.
I have no idea what this is saying.
Just as Alex gets to Jay, Tim resists and it becomes apparent to the OperAlex that they need to flee. Realizing Jay has been given powers, and to give him and The Operator some time to regroup and flee, Alex gives Jay the tapes he shot depicting him as a victim when he was actually an assistant, and The Operator then puts Tim under again to become Masky.
Why do they need to flee? What would Alex giving Jay the tapes do?
The rest of Season One then occurs here. Alex and The Operator, with the Marble Hornets crew save for Jay in tow, do several things out of Jay's sight, including possibly sending The Operator out to other Slendyblogs. Meanwhile Tim stays behind to antagonize Jay, all the while under the Operator's spell. Sometime before Entry 26, Alex is allowed to have a normal life again, with the reminder that The Operator could "pick him up" at any time.
The Operator is not Slender Man. He only exists in Marble Hornets canon. Further, why does Alex get to have a normal life if he's been under the Operator's spell for so long? And if Tim wasn't fully converted, when did that change and what made it go off properly the second time around?
Fast forward to Entry 26. Alex once again has a normal life with Amy. I'm going to assume that some time has passed since Alex has left The Operator, based on his reaction to the camera when Amy pulls it out. His reaction to me is not of someone who has successfully fled the Operator, it is one of someone who has worked with someone evil and is trying to move on. By this time, Jay has worked his way through Alex's tapes, and is now dealing with Tim. The Operator, realizing this, decides now it is time to pick up Alex, and this is what we see in Entry 26; not The Operator finally finding Alex and taking Amy, but The Operator taking Alex back under his wing in order to finally get rid of Jay.
So then what actually happened to Amy and why is Alex frantically telling her to run while running himself? Also, who put the camera back in the closet/was operating the camera at the beginning of the footage in 26?
Tim however has snapped out of The Operator's spell, thanks mainly to his medication.
So Tim wasn't fully under? Then why did the Operator abandon Alex?
Knowing Alex's real intentions, he attempts to stop Alex in Entry 35, but Alex and an un-knowing Jay defeat him.
What are those intentions at this point? To kill Jay? Why does the Operator want Jay dead?