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: 
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.
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.