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or were they only loyal to their primarch.


for example lets say there are a squad of white scars with Khan no where to be seen...and lets say this squad of white scars runs into Leman Russ

would they follow Russ' command or not?

Probably until they could be united with their brothers. Obviously, a lot depends on the context of the situation.

It was a pretty common occurrence in the Heresy days, what with Imperium Secundus playing host to a bevy of Iron Hands, Salamanders, and even a few Raven Guard who swore allegience to Gulliman.Check out the BL book The Unremembered Empire for the dish on that. Additionally in the Prince of Crows short story a former Raven Guard is named a member of the Kyroptera by Sevatar, and as such, sworn to the service of the Night Haunter. Additionally other chapters, in the years leading up to the heresy certain Legions took in Neophytes from other legions(the Luna Wolves) which began propogating the spread of the Warrior Lodges.The book Scars is where you'll find that. Additionally other battle groups sometimes had Primarchs that commanded small chapters of other Legions. The battle of Murder is one example, and there's a few others as well. Also, Space wolves were dispatched to all the remaining legions to follow around the Primarchs who remained "loyal" as a watchful eye on the remainder. Fear to Tread for an example. Usually if there was a Primarch around it was generally assumed that if a Space Marine said "I'm not going to follow that command," they wound up doing great dishonor to their fathers, ergo most Primarch-less SM listened to the nine foot death giants who command an entire legion of SM.

Chapters in more modern 40k universe will usually back the plays of 1st Founding Chapters in battle zones, or will at least take their counsel into advisement. Badab campaign saw deferment of the destruction of the Executioners chapter on the words of the Salamanders. The Dark Angels lead the campaign to purge the Fenris system of filthy viking heretics. Or preventing them becoming that I guess.