OK... so the plot of Serpent Beneath is centred around Omegon as he seeks to purge the Alpha Legion of the traitors/loyalists in their midst (ie. the ones who Omegon suspects of reporting back to the Emperor). Only... it's not.
Omegon identifies a leak from a secret Alpha Legion installation hidden in an asteroid that's being mined by the Demiurg, only it's not clear exactly who is doing the leaking. In order to avoid demoralising the Legion, and to be sure that they stop the leak, the decision is made to wipe out everyone on the installation in total secrecy. He and a crack team secretly infiltrate the installation and start killing everyone, with extreme prejudice.
As it turns out... it's not just any secret installation. This is the location of a powerful technological device that is capable of stilling the warp in the local vicinity, making the Legion's movements easy. In so doing, it has the handy side effect of causing warp storms elsewhere... in this case, "elsewhere" being the region of space where the White Scars are operation. The storms are not only trapping the White Scars in place, but they're preventing them from even hearing about Horus' rebellion. The Khan isn't even trying to get back to Terra - he doesn't know he needs to - but even if he did try, the storms would stop him.
Once nearly everyone on the installation is dead, the team wait for extraction. Only it never comes. Omegon isn't even Omegon - it's another Alpha Legion marine, pretending to be him (acting under his orders). The last we see of them, the asteroid has been redirected into a nearby sun, killing not only the installation garrison, but also the infiltration team... and destroying the artefact that's meddling with the warp, presumably (though we don't see this) enabling the Khan to learn of the rebellion and start heading back to Terra. There wasn't any leak - Omegon wasn't trying to stop someone feeding intelligence to the loyalists - it was all a cover, even though it was top secret in itself!
As if that wasn't enough circles within circles... Alpharius didn't even know what was happening, and is furious that the plan to keep the White Scars out of the picture has been defeated with the destruction of the artifact. This was all Omegon's initiative. It's not just that the Alpha Legion are backing Horus in order to follow up on the Cabal's plan and make things better for humanity in the end, as seen in Legion. It's not even that they've rejected the Cabal's scheming and decided to do their own thing, as seen in Deliverance Lost. It's that the Alpha Legion - even Alpharius/Omegon, who are supposed to be one soul sharing two bodies - are themselves divided, not supporting the Emperor, not following Horus, not following the Cabal, not even working together... but working against everyone, even each other, having a massive impact on the galaxy while they do so.
Since the Khan and his White Scars were instrumental in the defence of the Emperor's Palace on Terra (even though it tends to be Dorn and Sanguinius who get most of the headlines), it may even be possible that Omegon, acting in opposition to Alpharius, by releasing the White Scars from the warp storms they were encountering, changed the whole course of the Heresy in the Emperor's favour. What's he really up to? What about Alpharius, what are his real motives? Are either, neither, or both of them following the Cabal's plan? I don't know - but I am desperate to find out!
Anyway, the story was beautifully written and I found the layer upon layer (upon layer...) of conspiracy, counter-conspiracy, falsehoods, secrecy and lies incredibly compelling. Just superb IMO.
Oh - and there was also a bit at the end I didn't really get. Having lied straight to Alpharius' face about what's going on, Omegon returns to his quarters. There, his Alpha Legion armour is on a stand... and "another suit of armour" is on another stand, under a blanket. It read like that in itself was a big revelation or hint at some other theme, but I didn't really get it? (Though it's a long time since I read Legion).