From what I have heard, the Primarch that died on Pluto was Omegon as he was the one that wields the Pale Spear and the last Primarch recovered. The Primarch that is alive has been Alpharius, who was the first Primarch recovered.
At the end of it all, it doesn't matter who is who, because the Alpha Legion is all about deception. They were always there but never recorded. They fought for Horus but served the Emperor. Everyone claims to be Alpharius but not even they know who he really is.
For me, I want to know what their downfall is, what caused them to cease being a Legion. My best guess comes back to their deceptive nature. To quote Chernobyl: "Every lie we tell incurs a debt to the truth. Sooner or later that debt is paid."
The Alpha Legion falls because they never had a truth to begin with. They have no origin, no structure, no future. Alpharius was just a tool, no personal reason to exist. The Cabal gave him a purpose that he could decide for himself. They revealed to him the threat of Chaos, but he would not follow their plan, which is why he fucked over the Cabal. But while he had a goal, his Legion didn't. Some other Alpharius could go rouge because he was order to bomb a planet he brought into Compliance. Another one could have been exposed to the temptations of Chaos and saw their power as a reason to exist. Soon you have 15 different Alpharius's giving order and the whole legion breaks down.
The Alpha Legion may all claim to be Alpharius but they don't think the same as Alpharius.
For starters, The Cabal gave Alpharius & Omegon two futures: Horus is defeated, but the Imperium is slowly corrupted from the inside and eventually falls to Chaos (which seems to be the current course of the lore) or Horus wins, but he leads a rebellion against Chaos (lol) and leads to Chaos' eradication at the cost of humanity (which Xenos like the Eldar, who make up a portion of The Cabal, would benefit greatly from).
Not much of a choice, but I believe this choice shaped how both primarchs would conduct themselves during the Heresy. They both thought they were on the same page regarding this, but obviously not.
This leads to Istavan III and stories like
The Seventh Serpent, where the Legion is purging itself of Loyalists within its ranks.
Yet, at the same time, one of the primarchs is sabotaging the other by subtely giving aid to the Loyalists like the White Scars as seen in
The Serpent Beneath.
As for the "15 different Alpharius," that's by design. The legion did not break down because of that (they had been doing that even when they were the Ghost Legion). I do think that whoever was the Primarch during The Scouring figured it was best to "strike the tent" to ensure the Legion's survival (possibly curb the exposure of Chaos among the ranks at the same time) and intentionally scattered the Legion (rather than the violent breakups that occurred with the Night Lords or the World Eaters).
Perhaps "Alpharius" had to die to get the job done.
I REALLY hope once the Horus Heresy series is finished a deeper look into The Scouring happens.
I would love to see events like Dorn's crusade against the Traitor Legions are fleshed out (culminating in The Battle of the Iron Cage). Perhaps we'll see if the Eskrador campaign actually happened or if it was Alpha Legion propaganda.
The Alpha Legion protected the imperium... at any cost.
Including from itself (referring to the Alpha Legion. Or am I?).
On an unrelated note, the interest that YouTubers are taking into the Badab War is making me wish there were novels to go with it.
It's such an interesting event that is perhaps the most infamous Space Marine vs. Space Marine conflict since the Heresy itself and the birth of one of the most infamous Renegade Chapters of Chaos. Maybe we'll get there one day.
