Not much is known about the Salamanders’ role during the Horus Heresy by Imperial Scholars, save for their betrayal at Isstvan V.
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The Salamander’s role during the Horus Heresy is not well known to Imperial Scholars; what is for certain is that the legion, along with the Iron Hands and Raven Guard, was part of the first wave of attackers during the battle of Isstvan V. After the announcement of Horus’s treachery and the destruction of Isstvan III, the Emperor ordered seven Legions of Space Marines to attack the forces serving his former son and friend. But among those seven Legions, four were already traitors. The initial landing force fell into a trap and, despite their martial skills, the three loyal Legions were forced to begin a tactical withdrawal toward their landing site, which had been fortified by the four traitor legions forming the second wave.
At this moment the second wave opened fire on the retreating Marines, crushing them between the hammer of Horus’s forces and the anvil of the fortified drop site. Despite a heroic defense, the three loyal Legions were practically destroyed; all but a handful of battle brothers fell on that fateful day. First Captain Artellus Numeon managed to leave a scattered group of survivors off the planet, but their Primarch was missing.
After this sad defeat the Salamanders, as well as the other two betrayed Legions were largely unable to perform any tasks the Emperor had planned for them and spent much of the rest of the time of the Heresy rebuilding their forces. Vulkan was briefly made a captive of Night Lords Primarch Konrad Curze, but despite multiple executions the Night Haunter could not figure out a way to kill the Perpetual Primarch.
Eventually Vulkan was able to escape, and along with scattered survivors of his Legion they reorganized in Imperium Secundus under Roboute Guilliman. There they came across the shattered body and mind of Vulkan, who had his sanity restored after being stabbed by John Grammaticus wielding the Fulgurite, but apparently died in the process.
The Salamanders on Macragge thought Vulkan dead and placed him in the stasis-capsule Unbound Flame to lay in state, in preparation for funerary rites to be undertaken by his Legion. During this time, the casket was given an honor guard, which some of their number believed they heard a heartbeat from. Later, the Salamanders led by Artellus Numeon brought Vulkan back to Nocturne but were pursued by the Death Guard. After a brief but fierce battle, the Salamanders were able to resurrect Vulkan after Numeon provided himself as the final sacrifice.
Meanwhile, Salamanders (along with Iron Hands and Raven Guard) survivors of the Dropsite Massacre based on the Sisypheum began a campaign of vengeance against those who betrayed them, striking at Fulgrim and Perturabo on the Crone World of Iydris as well as Alpha Legion outposts.
Whilst the Salamanders altered their squad-level organisation to follow the strictures of the new Codex Astartes, they were able to retain much else of their Legion organisation – some say because there were too few of them to split into successor Chapters: The Salamanders are officially reckoned to have no descendants, though several Imperial scholars have pointed out various similarities in unit markings and tactical dogma in the Storm Giants and Black Dragons Chapters.
It is possible that these Chapters were created at some unknown, later date from stockpiled gene-seed, but whatever the claims, the Salamanders claim kinship with no other Chapter. Oft-considered the smallest Legion, the casualties of the Horus Heresy, plus their own highly stringent recruitment and indoctrination processes made not only their rebuilding seemingly glacial, but resulted in them coming in under Codex-approved strength for a single Codex Chapter. In accordance with Vulkan’ original reorganization of the Legion, the Salamanders Chapter is formed of only 7 permanent companies; each one nominally staffed at a little over the Codex-approved 100 Astartes. Nevertheless, the sons of Vulkan were able to forge themselves anew, and their steel has ever since been drawn in the defense of the Imperium of Man.
In the absence of Vulkan, the Captain of the First Company is considered the Chapter Master. This position is seen as a regency, however, and is occupied in the belief that it will one day be relinquished to the true holder of the position.
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