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Buckle in, this is going to be a long one.
What we know 100% about Alpha Legion:

1. Throughout the Great Crusade they operated extensively outside Imperium control areas
2. They operated secret, and powerful, industrial complexes
3. They had secret caches and bases scattered everywhere
4. Throughout the Horus Heresy they were moving East
5. Omegon is probably alive

So here now lets introduce the Perfidian Gap. Its an area within the East. In Horus Heresy Book Three - Extermination, the Alpha Legion were present in the genocide of the local xenos residing there. Fast forward 10k years and the area is now engulfed in a constant warp storms. Read this http://wh40k.lexicanum.com/wiki/Locrus.
Its super suspicious. A haunted planet next to the Gap, explorers vanished, no bodies, no signs of struggle, then daemons suddenly came, then suddenly left. And more importantly, why even mention this story? What purpose does it have? It doesn't really add anything new to daemon or dark angels fluff - so i think its actually there to add to Alpha Legion fluff.

I think the Alpha Legion is behind all this. There are instances where warp storms can be created, safe access through them to be found, and worlds within this storm being perfectly safe. I think within the Gap is a massive Alpha Legion stronghold. Alpha Legion is known to have all kind of weird tech, and I think some of it is possible to safely traverse this storm. I also think this method in which they do this can be relatively easily discovered, so they make every attempt at discouraging the Imperium from coming even close.

Also when Alpharius 'died' on Pluto - its said that Omegon sensed it half a galaxy away - likely in the East. I think Omegon's base, and the Alpha Legion's main base of operation, is in the Perfidian Gap. If this is the case, Omegon would most likely have legions of Alpha Legion space marines under his command, complete control over a very centralised and developed empire 10k years strong, hordes of human auxillaries, and 10k years of intelligence on the running of everything outside his domain.

What if large segments of the Alpha Legion - those loyal to Omegon anyway - stuck with him and didn't fracture. What if for 10k years they have been united in a common purpose. And the Perfidian Gap is in the center of all of this.

The hydra may not have a head - but things must always have a base of operation. If warfare is deception, then the Alpha Legion has made the best ruse - making people think they are headless. Their heads are just illusive and well hidden. Their guns, tech and recruits must come from somewhere. It takes entire worlds and systems, even sectors, to properly arm and supply a space marine legion. And by all accounts the Alpha Legion spent a lot of time invisible to the Imperium during the Crusade. If they don't get this stuff from inside the Eye of Terror as most mother CSM do, I think the Perfidian Gap is the answer.

Omegon spending 10k years building up a secret empire and network, waiting and ready for its moment, does sound like something the Alpha Legion would do.

Super out there theory: The Alpha Legion had a mini-civil war after the Cabal made contact. Omegon and Alpharius went their own ways. Alpharius and his boys attacked Pluto. He died and his faction fractured. Omegon and his boys moved East. He spent most of his time distracting all the forces in the East whilst the Perfidian Gap became fortified and shielded. Then when it was done, he went and got killed by Robbo. Now he's waiting for something so he can save humanity. Maybe the emperor waking up, maybe something else.

Of course maybe the Alpha Legion doesn't have warp storm tech, maybe Alpharius and Omegon were killed on Pluto and by Robbo, maybe GW used the Perfidian Gap for convinience purpose and they never actually thought this far ahead, and this is all one big coincidence. Who can actually say for 100%. But GW had made the Alpha Legion to be so mysterious and complex, there must be something there. If Malekith had a massive plot twist in the End Times, I do believe Alpha Legion will have one here too - damn that actually would really parallel one another. Understood bad guy is actually good guy all along and helps save the world.

Thoughts?

While interesting, and very likely that it is a bolt-hole for the Alpha Legion, I wouldn't so easily subscribe to it being an 'empire'. The entire idea of a consolidated power-base is not how I think the Alpha Legion would operate. I wouldn't be shocked, however, if they had some production facilities, R&D, training grounds, recruiting stock, and other things there. But a seat of power, like Macragge? Too vulnerable, too localized and centralized.

The Alpha Legion is an insurgency force, headed by an elite sect of Guerilla infiltrators. It doesn't really work in their favor to be an occupying force like the Ultramarines or Imperial Fists. They simply can't work well that way.

Here's an insane theory for you, though:

What if the Alpha Legion is Alpharius and Omegon?

It's alluded to several times that drinking the concoction made with their Primarchs' blood allows them to physically change to resemble him, even something I read about them being able to 'occupy' the bodies of other Legionaries.

I'm not sure I recall what happened to Alpharius' body, or Omegon's... but.... what if... they ate it?

The Alpha Legion is a sort of hive-mind, but not a unified one- a fractured consciousness spread across the entirety of the Legion.

Hmmmm, I like that idea. The hydra does not have a head.
But the Emperor made 20. I do really like this idea though.

There is only one thing that we know 100% about the Alpha Legion, and that is that we know nothing 100% about the Alpha Legion.
So yeah, there might be a huge unified Alpha Legion empire hiding in there. Or there might not be. It is certainly an interesting theory, but there is no way to know for certain, so I say you should believe what best fits the story you want to be telling.

I myself have always liked the concept of the Alpha Legion as an idea rather than as a single organisation. The original Alpharius, Omegon and Alpha Legion of the Heresy are all long gone. But the scattered survivors of the Heresy took up the mantle of Alpharius and spread his ideas and the traditions of the Alpha Legion to the new generations of renegades who rallied to their banner, thus creating several new Alpha Legions. And every time the Imperium crushes one of these Alpha Legions (the Alpha Legion has been declared exterminated many times), a few survivors may be left, scattered but able to pass on their ideals and traditions to others, thus eventually creating even more newer Alpha Legions. Like the heads of a Hydra, for every head you cut off, two or three more grow back.

The idea of having a secret base that has supplies recruits and some production makes sense. Not one but multiple though.

However not as a a seat of power. Too vulnerable.
One alone no, dozens of smaller, wide spread, not knowing many other bases makes sense.

More safe houses than fortress world and seat of power.