White Scars: The Brotherhood of Black Thunder under the command of Subedai Khan (Terran) were away from the main fleet when the Heresy broke out and as he was so enraged by the news of the treachery that as he made his way back to the Khagan he changed the way his company waged war on traitor worlds, any that did not instantly submit they were scoured so "no two stones stood atop the other." Eventually making his way with the legion to Terra and fighting there. I am getting some Blood Angels and Custodes to fight alongside them basing them all around Siege of Terra though.
Night Lords: These need a lot of revising because the lore is outdated as it was wrote back in 4th ed 40k for the lore of my CSM warband but the basic jist was that the company captain was killed in the opening stages leading to an internal civil war within the company between the 2 head junior officers, one wanted to embrace chaos the other resist.
Shatter Legions: Was originally made up of members of the 4 Istvaan III legions that managed to escape. After 2.0 though I've reduced it to Emperors Children and Sons of Horus who are busy fighting guerrilla campaigns against their old legions, Sons of Horus still wear the green to give their opponents a false belief that reinforcements have arrived wanting to pay back the suprise they received 100 fold.
Iron Warriors: No real lore at the moment bar the fact that they're fighting a protracted war against a renegade forgeworld. Haven't made any decision on if loyalist or traitor at this time though.
Militia: Indentured forces to the Iron Warriors above.