I've been working on some fan fluff for the missing legions and Chapters formed around it. Posting the general outline to gauge opinions on how well it fits in the story/background. Contains spoilers for any later stories I'll write. Names/events/etc taken mainly from Battletech, Game of thrones(a song of ice and fire), Tolkien, and 40k rumor/fluff/canon/etc~ sorry for bad grammar/spelling! Opinions Desired!
Primarch Aemon of the 11th Legion (Death's Hand) learns of his Legion/Home Sector's corruption/civil war and requests aid/council from the Emperor. The 2nd and 6th Legions (Legio Ursi"Legion of the Bear"/Space Wolves) are sent in response to assist with a purge of the sector.
Information gathered from initial battles between 11th loyalists/traitors reveals the extent of the Legion's corruption, and state of the sector in the aftermath of the civil war. The sector's planets have been Cleared/Purged of all life (by 11th Legion traitors during the CW) prior to the arrival of the Loyalist Legion's, only two worlds remain intact. Battle plans are formed; ground assaults upon both planets, followed by extensive bombardment.
Leman Russ assaults the world held by 11th Legion traitors under the command of 1st Librarian(if librarian is the correct term at the time) now turned Sorcerer "Vichtus Forel". He locates Vichtus and retinue in-ritual, and unknowingly finishes the ritual by slaughtering the present cultists, bringing warp-storms down on the sector. A Duel between Russ and Vichtus ends with Russ nigh unscathed and Vichtus in pieces.
Meanwhile Primarch Aemon leads a speartip of 11th legion loyalists against his Human Father/1st Captain Aemon Antonescu of the 11th Legion/retinue. Primarch Beor Mormont's "Old Bear" 2nd Legion in support, carries out the main purge of 11th legion traitors/auxilliary. A trap is sprung by Antonescu's retinue, killing nearly half of the remaining 11th legion loyalists, and subdues Primarch Aemon. Antonescu attempts to turn the Primarch willing (revealing the full extent of the warp's plans for the 11th and soon the 2nd Legion) instead of outright killing him/wounding him, and almost succeeds. Only failing when Primarch Mormont intervenes, duels Antonescu and saves Aemon from his fate.
The Warp storms summoned by Vichtus/his retinue consume the sector before the bombardment could be carried out, and all remaining loyalists are summoned back to imperial space. Primarch Aemon renounces his lordship over the 11th and sends the (roughly) 500 remaining loyalists to the Emperor, to do with as he wills. (he (Aemon) being unfit to lead them from his perspective). Aemon then boards a rogue trader and departs after expressing his gratitude to Mormont for his timely rescue, and warning him "Look to your Sector Brother".
the 11th Legion loyalists are merged into the 2nd, and the Legion/Primarch are officially stricken from Imperial Records along with the incident. The 2nd and 6th legions part ways, the 2nd returning to it's home sector. Meanwhile Aemon translates in-sector and plans an assault of one, chasing rumors of surviving 11th legion traitors in the 2nd legion's sector. Warp storms (mirroring the 11th legion's sector's storms) already threaten to consume the world and cut off the sector before the former Primarch makes planet-fall.
Aemon carries out a purge of the facility during the small window of safety before the storm fully consumes the planet, receiving updates from the rogue trader stationed nearby monitoring the storm. He slaughters the remaining 11th traitors/HQ, but is caught in a second trap to ensnare him in the storm/bring him into the fold. He eventually escapes but not before the storm consumes the planet/cuts the sector off from the Imperium.
The former Primarch appears aboard the Rogue Trader in the 2nd Legion's sector fleeing the storm, roughly a year later. He is alone aside from a few remaining servitors piloting the ship, having fought daemons/risen 11th legion traitors (to his dismay), emerging warp-scarred (somewhat like the Legion of the Damned but not Fatal/Life shortening due to Primarch physiology), but not corrupt (having found new strength/resolve after his last encounter).
Prior to the storms that cut the sector off from the Imperium, Mormont receives orders for all Loyalists to abandon the sector, and leave it to it's fate. Mormont willing to follow the orders instead calls for a vote amongst his Legion to stay or leave. The results of which are unanimous, to stay and defend the sector. Mormont and his Advisors/high command then decide they're unwilling to fully betray the Emperor. They send a contingent of roughly 5k Astartes with auxiliary to Terra with a message from Mormont. This consisting mainly of Terran born Legionnaires lead by 1st Captain Edwin Focht, and all remaining 11th legion Loyalists.
The Emperor decree's the 2nd Legion officially wiped from Imperial records for reasons separate than the 11th's erasel and folds the remaining loyalists into the Ultramarines until Post heresy. They form the nucleus of what will eventually become a minor Ordo (Ordo Fidelis) that mainly serves within ailing Chapters low in strength/the occasional overwatch of a suspicious chapter without overtly showing inquisition presence/concerns and causing undesired conflicts.
The Ordo builds support for an eventual Crusade to retake/re-establish contact with the sector, and have made successful supply/intel missions to the 2nd's warp-lost sector. Almost boarding on tradition, most chapters the Ordo serves with found a support chapters permanently attached to the main Ordo Force. This force carries out overt inquisition missions in larger scale conflicts, and will form the main Crusade to retake the 2nd's sector. Some examples; Anointed Templar, Fangs of Russ, Legacy of the Primarchs, Epitaph of the Fallen, among others.
After learning of events carried out by the 2nd legion in-sector prior/post to the mirror storms, Aemon swears to serve along side Mormont in payment for saving his soul. He takes on a new name "Mortuus Rex" and becomes Death's Hand. Now under a new title he fights in sworn silence alongside Mormont until the last 11th Legion traitor is perminantly banished to the warp.
The 2nd Legion's sector becomes a safe haven for presumed warp-lost vessals, maintaining a permanent pyschic beacon, and constant vigil via the intact and ever growing Loyalist fleet in sector. Basicly a bastion or plausible explanation for anyone that could possible survive, has survived, or that I'd like to survive (primarchs,heroes,warp-lost vessals). Even a possible reasoning for the primarchs to vanish mysteriously into the warp in the first place(they travel to this sector). A major section of the Sector is altered by the storms, and the planets within suffer drastic climate changes, turning into Ice Worlds.
Known enemies in the sector include the 11th legion traitors/daemon retinue, one of the largest Dark Eldar armies recorded outside of commorragh, dormant necron tomb worlds, traitors/daemons from the Eye, Eldar exodite raiding parties, and Feral orks growing in number after a space hulk passed through the sector. Ork survivors from Roks jettisoned by "Admrul" Hadrun da Kollida to colonize the system for later battles after he finds a good fight against an Ordo fleet that appeared in sector post heresy.
Other characters include 2nd Legion turned Ordo 1st Chaplain Janus Ascar Adurant or Chaplain Snow, who along with Master Librarian Hadrian Vessaire proves vital in the success of Ordo resupply/intel missions to the warp-lost sector (the Chaplain being a pure conduit and anchor for the Master Librarian to pierce the storm). Morgan Clearwater of the 2nd legion, who stayed behind with his Primarch (one of his advisors, possibly a chaplain dunno if they really existed before the council of nikea or if this time period would fall before or after the council). Franklin Osis, another warp-lost member of the 2nd with no rank as of yet. James Isaac Moreau, General of the Rabid Foxes inquisitorial regiment that serves alongside Focht's main Ordo battle-force.
Things I'm working out atm. How was the 11th initially corrupted, and by which god? Leaning towards Malal/Malice and the storms are his attempt to taint two legions and bring them into the fold. Names for the sectors and their locations. how early would the Necrons in system awaken? for instance, would some awaken during the storms or maybe they're triggered by an Ordo Fleet in sector on a mission (events usually flare up when the Ordo appears in sector).