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Not sure if this has been posted here yet as I've been mostly inactive on these forums for a while, but I've read over Forge World's Horus Heresy Book 3 - Extermination and by far the most interesting stuff had to do with Alpha Legion. It does a lot of typical "conflicting reports" and "not sure" stuff, but still squeezes in a lot of interesting new tidbits:

-The Legion may have been formed far earlier then originally thought (only a few decades before finding Alpharius) and during the early Unification Wars/Great Crusade there was an assassination/special ops force known as "Alpha Unit" which did not report to any known Primarch at the time. This force wore no heraldry and sometimes conducted false flag ops where they would dress up as another Legion

-Their gene-seed was specially crafted for an unknown purpose, and is compared in its uniqueness to that of the Salamanders and Space Wolves.

-The Emperor ordered their unique gene-seed line discontinued for some reason, keeping them at about 2,000 legionaries during the early great crusade. The book says this may have been for special gene modification in the future the likes of which no other legion saw.

-Curze said the Alpha Legion was "Hiding their true sins in a shroud of lies".

-During the Great Crusade the Imperial court was concerned the Legion was becoming "mad", conducting overly complicated/convoluted campaigns of subterfuge for subterfuge's sake even when a conventional assault would have been easier. They also apparently were concerned that the Alpha Legion was becoming "addicted" to manipulating lower non-imperial human civilizations into destroying themselves. Horus dismissed this however and seemed to like them.

-Shortly before the Horus Heresy, Alpha Legion withdrew into the fringes of Imperial territory. Also it is mentioned that their strength at the time of the Heresy was 120,000-130,000

-There may be some references to the 2 Unknown Legions in here. Specifically, there is mention of an aborted experiment with regards to gene-seed. The experiment is simply named [REDACTED]. Another passage tells of a Legion that as its gene-seed was about to go into mass production, "failed". Again, its name is simply [REDACTED].

Here: http://www.dakkadakka.com/dakkaforum/posts/list/594197.page
And here: http://www.dakkadakka.com/dakkaforum/posts/list/594174.page

I do find that part quite brilliant. It gives a lot of details, yet most of the answers are hidden and left to the imagination of the reader. That´s the way good fluff is written. It gives us a lot of new enigmas for the Alpha Legion, but in a subtle way, very far from the cheap solutions you read in some novels about the XXth.

This has officially made me want to buy all those HH books from FW.

I actually just researched the two lost legions yesterday after finishing "Horus Rising".

It seems the most supported fluff regarding them is that they had special gene seeds, as you said, and this caused them to do something so bad that the emperor removed all traces of their existence. Sanguinus was even afraid of becoming the third lost legion because of his legions genetic flaw.

Yeah this is interesting stuff. The Alpha legion in the Horus Heresy series seem very anti-hero, and Legion is quite good.

There was mention in one or two of the HH novels, (I am not caught up, I think I'm on twenty or Mark of Calth is the last one I read) where they hint that remnants of one legion were folded into the UM. Something about the size of the UM being far too great.

And there is of course references to the two lost by the other Primarchs, but no one wants to talk about them.

I'm trying to think of what would be so bad as to be wiped out of the record as opposed to galactic war, betrayal, and demon worship.

 Gorgrimm wrote:
And there is of course references to the two lost by the other Primarchs, but no one wants to talk about them.

I'm trying to think of what would be so bad as to be wiped out of the record as opposed to galactic war, betrayal, and demon worship.

Those two legions were badly painted, not worthy of being displayed in White Dwarf, therefore they were destroyed and their names expunged.

ROFL. Wow, I laughed a little too much at this one.