Theres literally no way you can watch the whole season and not be sure who killed baz. The only thing they left ambiguous was whether or not baz was js father. Ive read theories he is still. In the third episode of season 3, it is revealed he was shot to death by mia benitez. Pope investigates baz's murder with lucy's help and she introduces him to a man who claims to.
Skull And Bones Life After Death