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.

Eli's new position at the law firm means that he does not have an office, secretary or the power to take cases. Eli takes the case of a 15 year old boy whose mother was killed due to a medical malpractice by Dr. Agon. Dr. Agon worked at the hospital where Nathan works, Eli will have to sue the hospital. Jordan, in the meanwhile, assigns Maggie to be be Eli's head and so Eli has no choice but to take instructions from her. Taylor, however, organizes a live performance by George Michael to square things up with Eli.

Eli has a vision of an earthquake in San Francisco. Dr.Chen helps Eli realise that the quake is in the region where his client is planning on building a shopping mall by evicting the residents from their home. Eli understands that the only way to protect the people is by his client evicting the people by any means necessary even bribing the judge.

Eli takes up the case of a prisoner who is coincidently Keith's ex-client. Meanwhile, the law firm is visited by one of its partners, Marci Klein, who wants to investigate as to why the law firm was losing its Fortune 500 clients. This investigation by Marci could threaten Jordan's reign.

After the operation, Eli appears to have lost his visions. However, when an incident with a crane puts Jordan's life in danger, it's Nathan that starts having visions that may save his life... if Eli can convince Taylor to listen.

While handling the Sonoma case, Eli and Maggie deal with the change in their relationship and Maggie meets a new man.