What if the Lion held his Legion from reaching Terra in order to play it safe and see who would win (or maybe waiting for both sides to destroy eachother and he have the last strong legion). Maybe the "fallen" on Caliban were really trying to leave to aid the Emperor, and after the battle between Luther and the Lion, the "fallen" got spread out in the warp.
Now Cypher seeks to return the blade to the side of the Emperor like the Lion refused to do during the heresy, therefore fulfilling the legion's loyalty to the Emperor. That would explain why the fallen are hunted, because they would cast light as to what the Dark Angels really did.
This idea was in a thread a while ago, tried to get the basic idea of it.