Shiro is told by the fortune teller, who correctly predicts his promotion and random money findage, that the emperor will kill him. She dies telling him this. We don't know if she had any ulterior motive or if she was just a really accurate, really dumb fortune teller. (After all, she does pursue Shiro and as far as we know, gets nothing but dead out of it.)
The emperor may or may not have been planning to kill Shiro. He acted oddly, we never get an explanation. If he was planning to kill Shiro, we never get a motive. If he wasn't, we never get an explanation for the change of plans.
Shiro's death (first time around) produced enough energy to turn the seas to Jade and the forests to stone. We don't know why.
The rest of it is somewhat more understandable - he uses his uber powers (which he apparently had prior to his death as it took a powerful assassin sneaking up on him and the Luxon and Kurzick heroes to kill him) and his abilities as an Envoy to create a giant army of inflicted as part of some vague spell to bring himself back to life.
Did I miss something? I'm hoping that there's a cutscene I skipped that explains some of this because while I may have disliked certain things about the Prophecies storyline, it was never this sloppy. It's like MacBeth, only without the bits that EXPLAIN ANYTHING.
