When Omegon went after the big xenos pylon complex that can disrupt the Warp (I’m thinking Necrons), he destroys it, instead of letting Horus have it. Why? If he’s working with Alpharius, and wants to bring about the destruction of the Emperor and Humanity, so that everything else in the galaxy can survive, why would he destroy it?

Why does he have that little statement at the end of the story where he is the “snake in the grass”, and seems to be actively opposing his brother?

Why does he have another suit of Power Armor that "no one will ever see"?

Is he working for Chaos, and wants Humanity to survive so that Chaos can reign forever? Is he trying to secretly stop his brother and Horus? Is he really a mole planted in the Legion?

What’s going on here?

Discuss...

Recent Horus Heresy novels appear to display a 'split' within the Legion, particularly in The Serpent Beneath (The Primarchs) and this is the interpretation I intend to follow.

At the end of this story, Omegon mentions "The Third Paradox" presented in the vision/"acuity" shown to them by the Cabal.
The first two paradoxi (everything sounds better plural with 'i') are that the Emperor will live and the Imperium will stagnate and succumb to Chaos, dooming the galaxy, or that Horus will win, realise what he's done and destroy humanity and Chaos, saving the galaxy. Obviously, it's suggested that Alpharius and Omegon accepted this and so followed Horus to try and save the galaxy and destroy Chaos, acknowledging that although they are turning against the Emperor, The Emperor's main aim was to destroy Chaos.

What then, is the third paradox?
To me, the third paradox is that they are wrong to fight Chaos - both the Cabal and the Emperor - and that Chaos should be embraced, rather than destroyed. Humanity can unite under Chaos and grow powerful as a result. What if Chaos is the only way for humanity to survive in the galaxy, the only way to overcome the Tyranids, the Necrontyr, the Orks and the Young Races?

...

Additionally, when conversing with the cabal after being presented the vision/acuity, it was Alpharius, not Omegon, who did most of the talking and proclaimed their loyalty to the Emperor's main aim of destroying Chaos.

So whilst Alpharius was seeking to support Horus, Omegon instead may sought to have him fail (The Serpent Beneath). Afterall, how can two brothers, of such power as Alpharius and Omegon, remain on the same level, the same path through life, when all around them their brothers turn against one another? It's hard to see them remaining united in such a way, when all around them turns to chaos.
'[Trust] is most precious - and strongest - when it occurs naturally. Like between brothers,' Alpharius said.
'Tell that to Horus,' Omegon muttered.
'Fair point,' he conceded, 'Trust can be hard to come by, even amongst the closest of kin,' Alpharius let the point hang between them before moving on. From The Primarchs.