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Now, this is just a theory and I'm sure this has been started about ten million times before, but I'd be interested to hear others and I want to put my theory out there to criticism.

http://wh40k.lexicanum.com/wiki/Two_unknown_legions

I will be quoting for this page, it makes an interesting read anyways. I'll start by laying down the facts to begin with. So, there are 20 Legions created by the Emperor. All Primarchs are found, Legions created. Conquering galaxy etc.

1. Two Legions are missing by the time of the Horus Heresy. Horus has 9, the Emperor has 9
2. It is said that fully half of the SM Legions turned to Chaos
3. In front of the Imperial Palace on Terra the plinths of II and XI are empty and 'their separate tragedies' are never spoken of
4. Nothing as strong as a SM is ever fought by the Imperium before this time

Another point is that Horus damages tank XI when being given a vision by Erebus, he is then sucked into a Chaos vortex. This may not have much of an effect on my theory, but it can be used.

My theory is that one of these two Legions turned to Chaos and the other was sent to destroy it. In the process they completely annihilated each other.

As XI is damaged by Horus, the seal may have been broken and the Primarch was exposed to the Chaosy badness as it was teleported to a random part of the Universe. Whether this happened or not is up for debate, but whatever happened, one Primarch was influenced by Chaos. This Primarch then openly turned after creating a full Legion, the other Legion, lead by its Primarch is sent by the Emperor to deal with the traitor in whatever way (negotiation or death).

The full fury of two SM Legions fighting each other would have been brutal and unheard of in the Imperial Universe. However the gargantuan battle involving 20,000 marines would be titanic, so whoever won would only have done so by a small margin (Primarchs are not usually known for tactical ineptitude, except maybe Angron). Complete mutual annihilation is unlikely, so if the Imperial marines won, the few survivors would be maybe purged for purity reasons or integrated into other Legions, maybe kept on Terra, who knows?

If the Chaos Legion had won, the Emperor would likely have personally have lead an assault on the traitor Primarch's forces and wiped them out, they would likely be crippled and in no shape to fight another Legion.

Given the shock and horror of the turning traitor of an entire SM Legion, all records of them would be destroyed so that they could never be remembered. The Legion that remained Imperial would have been broken up and/or destroyed. The shock of losing an entire Legion in one titanic conflict would have been too shocking for the Imperium's population to know about or even reflect on in the future (as they didn't know it would happen again), so all records would have been destroyed so that the conflict would never be looked into. All events involving it would have been covered up.

Throwing it out to the floor now, have fun and don't be too harsh.

There was a massive threadnaught on similar lines not so long ago. To reiterate part of what came very true from that. Both of the missing legions and primarchs participated in the great crusade. But at some point during those 200 or so years "something" happened that was so bad that both of their existences or information on them has been expunged from record.

WhiteBishop wrote:2. It is said that fully half of the SM Legions turned to Chaos

People take this to mean 'exactly half' of the original 20 Legions... which, IMO, is reading to much into it. It's a fairly casual turn of phrase, which could mean exactly half, about half, or more than half.

It could also, since all records of the missing 2 have been deleted, be ignoring those two altogether. (As an aside, older fluff mentioned that they probably fought on Horus's side, at least at the start of the Heresy, but this has since been retconned by the Horus Heresy books.)

WhiteBishop wrote:20,000 marines would be titanic

It would be alot more than that, these are legions we are talking about.

But why would the tragic hero of the imperium be deleted, with the strong history of hero worship in the imperium they would have never forgotten him or the legion

This question turns up from time to time, and can be answered in only one way:

Games Workshop never developed the two missing legions, and never will.

Leaving components of a game blank serves three purposes.

1. It allows future developments to be added at a later date, thus asllowing a casuse and effect without a direct retcon, as you link a future design idea to a opast concept that wasnt fully described.
- This was mentioned in completeness because Gw does this a lot, however it isnt what they did here.

2. Leaving areas blank allows an air of mystery, thus ading depth to a background by omission. This is 'cheap' and as the depth is defeined by a lack of data rather than a presence it automatically attempted to fit any surrounding stories, thus strengthening continuancy.
- GW did do this in this case but it wasnt the primary motive.

3. Blank areas allow players to develop their own input to cannon independently and individually without interfering with canon. If you decide to put your own interpretation to ultramarines you can be 'wrong', if you add your own interpretation to a blank legion you cannot be.
- This is the reason the two unknown legions exist, it was confirmed as such in old White Dwarfs from the Rogue Trader era.

Blanking ias a common tool of games designers first seen in Gloranthan Runequest. Whole nations were named marked on the map and from then on left blank. This way no publication would ever say miore than confirm thier existence thus allowing players to develop the lands on their own knowing that their efforts will not be contradicted by future published canon.

The two missing legions were Blanked as a games design tool. This will not change. So you can make of them what you will, you will never be right, newver be wrong and never have canon confirm or contradict you. Have fun.