Shadowkeep is like the teaser of the main story, while Beyond Light is the trailer and Witch Queen is the first act...
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Shadowkeep has like 2 story arcs going on. You got the Darkness return and Vex of sol devisive darkness worshiping vex. You had a different arc the scarlet keep,Hashaladun, Pit of Heresy. Everything related here was just a manipulation of Savathun to kill of the Hive on the moon. The hive on moon are of Oryx/Crota brood . Savathun hyped them up to make the scarlet keep gave Hashlasun Zolmak PoH boss. So that earth guardians would come back to the moon and kill them off.