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It has long been supposed that since Alpharius was only familiar with one other Primarch, Horus, it was self-explanatory why he chose the side he did at the outset of the Heresy. Indeed, the very plan at [[Isstvan V]] where Horus struck his first blow against his fellow Legions by destroying most of the [[Iron Hands]], [[Raven Guard]] and [[Salamanders]] Legions in a massive ambush, was very reminiscent of plans that Alpharius had created in the past.{{Fn|2}} However, it is possible that there is another reason for Alpharius leading his Legion to the side of the traitors, a secret known only inside the Legion. Around two years before the beginning of the Heresy, Alpharius Omegon was apparently contacted by members of a [[Xenos]] organisation called the [[Cabal]], who brought to him visions of the impending civil war within the Imperium, and expanded knowledge of the nature and designs of [[Chaos]]. It is believed that the Cabal convinced Alpharius that the only way to permanently defeat Chaos was to ensure that Horus was victorious. It is perhaps for this reason that Alpharius Omegon, secretly true to the Imperium and loyal to the Emperor, may have chosen to join the heretics.{{Fn|1}}
Further during the Heresy, the [[Cabal]] sought to lead Alpharius Omegon behaviour in order to make Horus victory easier. One of such actions was the ordeal against the [[Raven Guard]] with the intent of preventing [[Corax]] to rebuild his legion after the blow struck on [[Isstvan V]]. Some [[Alpha Legion]] marines were infiltrated, under the direction of Omegon, in the Raven Guard thanks to Alpha Legion apothecaries grafting the facial traits of some dead Raven Guards over the face of their own legionaries. Once known, through their infiltrators, that the original genome of the Primarchs was in the hands of Corax, Omegon acted in order to recover the secret knowledge so that the Alpha Legion could be expanded in future times. With the help of renegade Mechanicum magos Unithrax, the Alpha Legion tainted the original genome recovered from the laboratories of The [[Emperor]] on [[Terra]]. This was accomplished introducing a virus-vectored mutagen based on daemonic blood making the successive Raven Guard implantation's result in operational but deeply-mutated Astartes exhibiting scales, horns, fangs, tails, overgrown muscles and similar features. Meanwhile, Omegon bound to his service, although not directly consistent of the fact, both a renegade Mechanicus faction and some representatives of the ancient and noble guilds of [[Kiavahr]]. He pushed them to [[Battle of DeliveranceRavendelve|open rebellion]] against the Raven Guard and, in the chaos resulting from the battle, he personally recovered all data stored in Corax laboratories as well as the tainted original genome. In the aftermath, Alpharius was obliged to give the obtained data to Horus who handed them to [[Fabius Bile]] for deeper research. What Bile did not know, was that the data were practically useless since incomplete at best. Of course, the Alpha Legion kept for itself the integral data as well as the corrupted genome. The Plan of Alpharius had always been to use the Data to rise the Alpha Legion over all other legions, loyalists and traitors. After this action, Omegon left the Cabal representative [[Athithirtir]] on board his ship into the void stating that the legion would fulfill its engagement on its own, without external interference or control.{{Fn|3}}
Later in the Heresy, Alpharius dispatched forces to attempt and block the [[White Scars]] from leaving the [[Chondax Campaign]] and joining loyalist forces. Despite a fierce battle with the White Scars these ships may not have been armed, further compounding the true nature of Alpharius and/or Omegon.{{Fn|6}} Alpharius went on to [[Battle of the Alaxxes Nebula|corner]] the [[Space Wolves]] under [[Leman Russ (Primarch)|Leman Russ]] himself, nearly destroying them and dueling Russ disguised as one of his own [[Lernaean]] bodyguards. Victory seemed certain for Alpharius until he was forced to withdrawal after the loyalists received [[Dark Angels]] reinforcements. {{Fn|8}}
