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In every book I read about w40k, 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 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?

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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

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