Like the other anon said, it's a big mystery but one of the theories is that the Dark Angels of the present are descended from the marines 'exiled' to Caliban during the Great Crusade. (The Lion would basically send back people who gainsaid him ostensibly to be garrison and train new marines for the Legion.) The marines who joined Luther's rebellion changed their black armour to green, while the Lion's marines kept wearing black.
There's a chance that the Calabanite Dark Angels had a change of heart or realized they were on the losing side of history and turned their cloaks again. Now they're hunting the Fallen who were scattered through time by the Ouroboros, Tuchulcha, and the unnamed third Warp engine out of shame, guilt, and a desire to hide their past treachery from the greater Imperium. At the same time the Fallen are not a monolithic group with aligned goals, some were always loyalist, some are Chaos-tainted, some are just renegade, some have changed their minds in the intervening years, etc.