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So i have been trying to read up on the alpha legion stuff, what exactly is the conspiracy/ fan theory about them actually still being a loyal chapter?

Could some one provide a TL;DR?

Alpharius and Omegon met a xenos organization known as the Cabal. It was foreseen by the Cabal that should Horus win, Lorgar's goal of humanity becoming fully symbiotic with chaos (ie. every single human becomes Gal Vorbak). Horus would be appalled by this, regret his decision and wipe out humanity in the process. Chaos, at this point tethered to humanity, rather than the warp, would die alongside humanity. Thus the Alpha Legion should ensure Horus wins to destroy chaos in the long run.

The plan was not pro-humanity, but it was anti-chaos.

It is left vague whether the two twins actually agreed to the plan, or are just going along with it. It's been foreshadowed that there will be a schism between the two brothers regarding this. Furthermore, it's unknown what percent, if any, of the rest of the Alpha Legion is aware of this plan.

However, because plenty of people only learn 40k lore through memes, this got condensed into, "The Alpha Legion are secret loyalists!"

In the novella Seventh Serpent, it is stated outright that there are loyalist Alpha Legionnaires and implied that one of the twins is also loyalist.

There is also a (very) loose theory about either Alpharius or Omegon being the first Grandmaster of the Grey Knights. He was named Janus after all...

Also note that the Alpha Legion is not necessarily all on the same side.

The Serpent Beneath has Omegon ordering a covert operation strike by the Alpha Legion against another Alpha Legion facility.

Equally, the two Alpha Legion fleets one sees in Scars seem to be acting in opposing ways - the ones attacking the Space Wolves would be implied to be traitors, but the ones blockading the White Scars but not attacking, and thus ensuring they got all their messages, not just rushing off after "Russ has attacked Prospero, help us!" are arguably acting in the loyalists' interests.

locarno24 wrote:
Also note that the Alpha Legion is not necessarily all on the same side.

The Serpent Beneath has Omegon ordering a covert operation strike by the Alpha Legion against another Alpha Legion facility.

Equally, the two Alpha Legion fleets one sees in Scars seem to be acting in opposing ways - the ones attacking the Space Wolves would be implied to be traitors, but the ones blockading the White Scars but not attacking, and thus ensuring they got all their messages, not just rushing off after "Russ has attacked Prospero, help us!" are arguably acting in the loyalists' interests.

And in "Seventh Serpent" the Shattered Legions find themselves in a conflict between the AL loyalists and traitors. Alpharius and Omegon are really playing against each other, it seems.