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When [[Raven Guard]] Commander [[Branne Nev]] arrived at [[Istvaan V]] to retrieve several of what remained of the Loyalist forces including his [[Primarch]] [[Corax]] , the Alpha Legion tried to help Corax escape, going as far as killing the commander of a [[World Eaters]] [[Battle Barge]] which could have delayed the superior [[Raven Guard]] fleet.{{Fn|10}} The Alpha Legion had [[Apothecary|Apothecarii]] that were masters of face transplantation. They took the faces of fallen [[Raven Guard]] Marines to transplant them onto their own [[Space Marines|Astartes]]. Together with the knowledge gained by digesting the brains of the dead [[Raven Guard]], three Alpha Legion Astartes were able to infiltrate the [[Raven Guard]] Legion.{{Fn|19a}} Later about 50 ''Alpha Legion'' Astartes in the colours of the [[Raven Guard]] were sent as reinforcements for this these agents.{{Fn|19b}} While [[Omegon]] could retrieve the data these infiltrators obtained, all of them were killed by the [[Raven Guard]].{{Fn|19c}} Learning of the infiltration of the [[Raven Guard]], [[Horus]] ordered [[Ezekyle Abaddon]] to find Alpha Legion agents inside his own Legion at all costs.{{Fn|19a}}

During the [[Horus Heresy]], the Alpha Legion split off from the main body of [[Horus]]' forces early and did not attack [[Terra]], instead embarking upon a series of delaying actions in an attempt to hold [[Imperium|Imperial]] reinforcements in place. A notable earlier example was [[Chondax Campaign|attempting to block]] the [[White Scars]] at the [[Chondax System]], but [[Jaghatai Khan]] was able to maneuver manoeuvre out of their trap.{{Fn|28}} [[Alpharius]]' or [[Omegon]]'s dubious agenda came to light at Chondax, where they were under orders from [[Horus]] to recruit the White Scars. Instead, the Alpha Legion fleet there engaged in hostile actions to seemingly provoke the Scars into a fight after blockading them long enough for them to get word from [[Rogal Dorn]] of Horus' treachery. Indeed this message was only delivered because Omegon had dispatched despatched forces to destroy an Alpha Legion-occupied [[Pylon]] array blocking the White Scars' communications. Subtly, the Alpha Legion or at least elements of it made sure that Jaghatai Khan would join the [[Emperor of Mankind|Emperor]].{{Fn|28}}{{Fn|11f}} Not even the Alpha Legion itself was spared from their own schemes. Alpharius was able to manipulate a strikeforce of members of the [[Shattered Legions]] under [[Shadrak Meduson]] into eliminating a cell of seemingly loyalist Alpha Legion.{{Fn|32}}

[[Alpharius]] was eventually charged by and with [[Horus]] himself to spearhead the traitor advance into the [[Sol System]]. Alpharius himself [[Battle of Pluto|led a large fleet against Pluto]] in the opening shots of the [[Solar War]]. During the battle, Alpharius was seemingly killed by [[Rogal Dorn]] but [[Omegon]] effectively took over his responsibilities.{{Fn|31c}}

[[Alpharius]] later reappeared during the muster of traitor forces on [[Ullanor]] in the prelude to the [[Siege of Terra]], giving [[Horus]] a detailed map of the [[Sol System]]'s defenses before quitting the war effort.{{Fn|34}} After the setback at Pluto, the Alpha Legion defied Horus' orders to muster for the [[Siege of Terra]] and instead delayed [[Roboute Guilliman]]'s advance as he attempted to reach the Throneworld.{{Fn|73}} In order to delay Guilliman's advance, the Alpha Legion's strategy was focused on seeking loyalist vessels, especially from the Ultramarines, and appear in overwhelming numbers to forcibly redirect them into perilous [[Warp translation]]s, all the while avoiding being drawn into open conflict. Guilliman's fleet was forced to intercede to allow supporting Loyalist forces to advance, further delaying him from intervening at the Siege of Terra.{{Fn|84}} Despite Alpharius's absence from the [[Siege of Terra]], scattered Alpha Legion elements are known to have taken part in the traitor effort.{{Fn|75}} In addition, an [[Ingo Pech|Alpha Legionnaire identifying himself as Alpharius]] was seen alongside [[Actaea]] in her attempts to aid [[Ollanius Persson]] and [[John Grammaticus]] in their quest.{{Fn|67}} This Alpha Legionnaire informed the group that his other brothers on the planet that were now activated would aid them in fulfilling their objective.{{Fn|69}}