Eli Stone finds his life at a crossroads and soon learns that he suffering from an inoperable brain aneurysm that's causing his hallucinations. Struggling to cope with the news, Eli begins to have visions that he is a prophet and decides to use his new found abilites for good.

While Eli takes on a lead paint manufacturing case that may take him to the Supreme Court, Jordan is forced to defend his sanity in court. Meanwhile, Eli discovers his father's diary that contains a disturbing revelation.