Question: In every book I've read about Warhammer 40K, the Alpha Legion always have a finger in everything. I have read occasionally that they have a secret agenda in connection with some alien council, but if that's the case, what is it with the tentacled guys completely fallen to chaos? I thought they were neutral or something. What is or can be their main purpose? Any ideas?

Answer: 
The Alpha Legion are unique amongst the various Traitor Legions - they followed Horus in his heresy, but then did not follow the other Legions into the Eye of Terror.

It is possible that they are still loyal to the Emperor (but not to the Cult of the Emperor) - but while they have not wholly fallen to Chaos, they still work with the Chaos Legions and help spread Chaos Cults.

[Warhammer 40K Wikia site - Alpha Legion article](http://warhammer40k.wikia.com/wiki/Alpha_Legion)
The alpha legion was lead by 2 twin primarchs the kabal an alien counsel showed them that if horus lost the hersey chaos would win so the sided with him. They still side with the emperor because they are fighting for the greater good. (If horus won the mortal in him would have snapped and killed every human left alive to remove the taint of chaos and starving the gods what they need to stay powerful so they would be about as powerful as a greater daemon at most)

I got this all from the [40k wiki](http://warhammer40k.wikia.com/wiki/Alpharius_Omegon) so look there for proof.