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So, I have been bouncing around an idea, that if I do ever decide to make an army, I will focus on making loyalist alpha legionaires, simply because I got caught up in the rapture about them actually being loyalists, but sacrificing themselves in order to destroy chaos. Now, in order to play with these little guys, my question is what SM codex best represents their tactics? Now, considering the fact that they use local forces in their attacks, I suppose I should also consider allies, as well, shouldn't I? Also, considering the chaos version has kept the legion color scheme, I have been thinking of making a new one, in order to symbolize their purity and wish to prove themselves from those alpha legion members that actually have fallen to chaos. Any suggestions?

Ironically, I would suggest the Chaos Codex, as it gives you access to marines and cultists (which could represent Alpha legion agents). Or if you are not adverse to allies, vanilla SM allied with Grey Knights so you can use the acolytes to represent agents.

I say just compare the two codexs and choose the one that you think suits the alpha legion better. If you like both than you can just take allies from one and use the other as your main codex

If you want to go the forgeworld route you can use Tyrant's Legion. That list would let you run a pretty good variety of forces from pre-heresy marine legion to local militia to standard codex marines.