Who set up Hightower?
We know that agent O'Loughlin followed Red John's orders to kill Timothy Carter, and that Red John elaborately arranged the plot to frame Agent Hightower for it.
At the end of the episode entitled Red All Over, Bret Stiles visits Hightower's office asking her to reprimand Jane for his behavior. Both she and Jane brush him off. Stiles leaves in a huff (we never see him lose his cool in any other episode) after issuing a subtle threat. Does Bret Stiles issue empty threats?
We know Red John doesn't.
Hightower is returning to the series in episode 6.4, "Red Listed." All will be revealed....
(Well, maybe not everything during that episode, but soon)
