I was thinking of the Warmaster in the strategic sense. The one who plans the campaigns and dispatches the legions to their various objectives. Since Alpharius would be making these decisions then he would be Warmaster even if the orders appeared to be coming from the Emperor.
I understood what you meant, I was just pointing out that the position of Warmaster is just as much political as strategic.
My plan would be for Alpharius to buy Magnus' silence by offering him what he wants - the freedom to continue his research and modus operandi without a witchhunt against him and his Legion. Such was Magnus' vanity and certainty that what he was doing was right, I think that Alpharius offered him a deal for his silence that he'd take it.
But since Magnus doesn't think he's doing anything wrong why does he need to make a deal? Why should he have to help Alpharius to get what he deserves? Plus, the Warmaster's approval should indicate the Emperor's approval. Which I think Magnus would be interested in making official (see below), meaning he'll get in contact with the Emperor. Meaning that Alpharius' contradiction of Nikea will be exposed. Meaning Alpharius will be boned.
Magnus may see this as a positive sign that his knowledge and power was being accepted by the Warmaster himself.
But not officially, since officially there is no Warmaster.
No more having to defend himself against Mortarion, Leman Russ and Rogal Dorn who hated the idea of Librarians
Except that since Alpharius' condoning of Magnus is a secret but Nikea remains a public act, Magnus must still face the condemnation of his brothers who still have every reason to believe that they were right.
If he went via a proxy then the contact methods could be intercepted.
I think it's pretty safe to say he went through a proxy. But then, so are millions (if not billions) of other people. That's a lot
of proxies the Alpha Legion have to intercept. Do they have the man-power to do that, infiltrate the Legions and still appear to be an effective military force?
That being said, I didn't think that the Warmaster did command the Mechanicum although I could be wrong.
Maybe command was the wrong word. Horus and Kelbor-Hal seem to have worked pretty closely during Horus' run as Warmaster (that's how he got turned) and it certainly makes sense that the Warmaster would have to be involved pretty closely with the guys responsible for making and shipping his weapons.
However such is the skill of Alpha Legion that I believe that given a few years as sleepers then these operatives would be successful in hacking the Legions communication methods.
Certainly possible. There is going to be a period before those operatives are operational though and in that period (potentially a couple years as you point out) the Alpha Legion are flying blind.
Quietly assassinate someone who has the skills needed, eat them and hey presto.
You do realize that you just suggested murdering perfectly loyal soldiers of the Imperium right? And cannibalizing them! Just so that the Alpha Legion has the opportunity (not necessarily the ability) to infiltrate a completely loyal Legion so as to manipulate it into continuing to be completely loyal. Just... no.
The Space Wolves, Blood Angels, Death Guard and of course the World Eaters would present their own problems but I'm thinking facial implants to disguise as the Space Wolves, face transplants for the Blood Angels, cosmetic non functioning Butchers Nails for the World Eaters for appearances sake and I'm not sure about the Death Guard due to the poisons - I'll come back to it
The problem with faking these Legions isn't how much you look like them (that's easy) it's how much you think like them; whether or not you can fake their tactics convincingly. Can someone without the Nails keep pace with the World Eaters? An Alpha Legion infiltrator almost shows his hand to the Raven Guard by using a move they're not trained in during a combat simulation. Can they keep themselves from doing similar things within these Legions, or others whose tactics (down to the individual level) are likely to be very different from what the operatives themselves ere trained to do? Especially in the face of suicidal orders? A World Eater (and probably a Space Wolf and Blood Angel to a lesser extent) wouldn't question an order to charge into the face of overwhelming opposition, they wouldn't even hesitate. But that's not the way an Alpha Legionnaire is brainwashed to think, so they will hesitate. The operatives are going to run into this problem in every single Legion. At some point they are going to be expected to do something that they were never trained to do (or were trained not to do).
Since the Emperor was concentrating on his Webway, as long as the crusade continued the way he wanted and Alpharius could justify what he was doing then I don't see why he wouldn't be ok with it. Again we don't know for sure but since the Emperor was non contactable much of the time then I think he'd be happy.
The problem is that your rational for the Emperor choosing Alpharius is that he knows Alpharius will be able to keep tabs on his brothers, meaning that the Emperor has to explicitly approve of this infiltration (and now, assassination) before he picks the Warmaster. I just don't see him being willing to do that.
This is just my theory and I'm trying to cover any holes discovered as much as I can. Hope this is ok? I'm having fun expounding on my theory
Of course, but in order to develop a solid theory and cover any holes, someone has to show you those holes. That's all I'm doing, asking questions.