Board Thread:Warhammer 40k General Discussion/@comment-185.37.86.69-20160206091809/@comment-26516936-20160208091310

It's almost certain that at least one of the twin primarchs has survived & quite possible that both have. Gulliman killed someone who he thought was Alpharius but it could have been an Alpha Legionary buffed up with toxic drugs & tech to something close to primarch level. The Alpha Legion regularly used dopplegangers to fool others into beliving they were dealing with Alpharius & while fooling another primarch would be more difficult it's probably within their capability. Making a legionary capable of going toe to toe with Gulliman now - that would tough. But given the resources that the Alpha Legion had it's certainly possible that they could do it, though any such transformation would likely be short lived & end in killing the altered legionary rather quickly.

All in all we can say it's almost certain that at least one of the twins is still alive - though if only one does survive which one is anybodies guess. My theory is that the surving twin (or both) returned to their hidden homeworld - which was never discovered during the Great Crusade - & has been manipulating events from there ever since.

As to the loyalty of Alpharius/Omegon thats as hard to figure as Cypher's (who happened to be allied with the Alpha Legion for a good while at one time). It's true that many Alpha Legionaries have turned completely to chaos (Voldarius comes immediately to mind) many more have not. Most of the time Alpha Legion operatives use Chaos & it's minions to further their agenda but most of them don't serve it. In fact it's quite possible there are two Alpha Legions, the public one that is the enemy of the Empire & formenter of chaos & a hidden one that is manipulating both sides with the goal of ultimately defeating chaos. In fact given the proclivities of the Alpha legion it's likely most, if not all, of the formenters of chaos would be completely unaware of Alpharius/Omegon's true aim in such a scenario.