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)
Read Legion- it is amazing and starts with a "Yo mama" joke. 

The alpha legion are a great example of why the heresy had to happen. They understand that only through eternal conflict can the human race survive and thus balance out the war. As the 20th legion they had spies everywhere so that depending on who was in ascendency they could always nudge things back in the right direction- that is to say towards a draw. The book Deliverance lost is one of the best examples of this- they wait to see which way the raven guard go before making their infiltration known.