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Here goes lucky number five on my attempts to create fluff for my CSM chapter, I don't really have a name for them yet, but I've got some of their backstory:
Since its beginnings the chapter has been a shell for the Alpha Legion, a base from which to launch operations and a influential organization from which to direct the flow of politics in the area. The chapter is officially listed as being an Ultramarines successor, but in reality the Ultramarine Gene-seed was switched in transit with Alpha Legion seed. The Ultramarines who were supposed to train the new chapter were also replaced by Alpha Legion marines, and the current chapter master is a lord of the Alpha Legion going by the code name "the Master of Shadows". From their base the chapter recruits initiates who fail their tests as Alpha Legion agents, and give them new lives and identities to carry out the Legion's business. There is no telling how many people, even entire families are secretly working for the Alpha Legion, or worse: they don't even know they're agents.
Inquisitors who investigate too closely are mind scrubbed until they are singing the praises of the chapter, a good thing because behind the mask of a codex chapter, chaos lurks. The chapter is also known to create clones of people for infiltration operations, but there are a group of clones who are very special to the chapter master. They are his clones, and the source of his seeming immortality. Mentally they are all him, or at least a human him (who knows how much humanity has rubbed off on him during his many lifetimes) but physically they are how he would have looked had he stayed human, but upon his death that changes. Hidden within their genetic code, in the junk DNA that doesn't normally effect humans, there is a code for a psychic link between the clones and the chapter master, and upon his death a second DNA code activates, rapidly transforming the clone into an astates. At that point the memories of the chapter master enter their mind, and they become him fully. His family, who are always unknowing agents of the Legion activated by the sight of the new chapter master, lead him to a set of power armor in a hidden compartment somewhere in their home, and the new chapter master dons the armor before returning to his chapter to begin the cycle anew.
So what do you think? Is this finally acceptable?

Sounds good so far.

Yay, finally acceptable! Now I've got the color scheme, it's supposed to be close enough to the Alpha Legion's that at a distance they're indistinguishable, so the chapter with it's pet inquisitors takes any repercussions from imperial agencies, and if anyone starts snooping around they're quickly "invited to Lake Logai" if you catch my drift.

EDIT: seeing as I have some kind of mind control conspericy going on here, why not push it further and have the current chapter master be involved in a very silly chaos cult (based on discordianism) while he was still human? Then when he becomes an astates he uses the silly cultists to spread chaos's message.

Sounds neat, may need to run up some stolen eldar tech into the soul-switcheroo. The name I came up with was the Serpent's Shadow chapter, you know, hydra and all. Whaddya think?

Yea that's nice. They'll be called the Serpent's Shadow.
And as far as the soul switcharoo there is none. The chapter master and his clones are psychically linked, one is aware of this, and the clone has the memories locked in his head. When the original died the locks keeping the memories hidden opens and the clone can access them. As far as the soul the original one before he was even chapter master ascended to become a demon prince. The dead one's souls merge with him.

Neat. Well, glad I could help with the name!