As a sand box game, I really just follow the characters interests for scene development, but the meta plot was as follows:
An Order of Hermes mage was secretly a Nephandi, but struggling with his own dissolution. Not yet fully committed to his fall from grace, he tried to do good but things would go awry.
Meanwhile, the Syndicate tried a bold new tactic, to lure potential reality deviants, identified through big data analysis (although that was imperfect, and often gave them only rough addresses). Then, they would be tested through sudden and shocking stress (I.e., police brutality). The true deviants would this be separated from the citizens.
So next the torn cloth would lead you to the Black Pyramid chantry, where you might figure out who your paradox causing rescuer was. I was going to use this as a wedge to bring you into chantry politics, and see what drew your attention, although I hadn't yet planned what sorts of Tradition-shenanigans you would uncover.
Once I had introduced you to that larger community, I was hoping to spring a larger conflict - I have no idea what that would be, but I was slowly leaning to Orphan-terrorists.