Eli goes in for an operation on his aneurysm, but it doesn't go as planned and Nathan is left with a difficult decision.

Eli has a vision of traveling in a car when all of a sudden an earthquake hits the Golden Gate Bridge. Eli tries to warn people but nobody believes him until he meets Daniel Foote, a scientist that predicts the earthquake. Eli and Daniel try everything they can to shut down the Golden Gate Bridge by suing San Francisco only for Marci Klein to oppose them.

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.

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 visions take him way back to the day when his father died. It was the same week when Eli's brother, Nathan, was sued for carrying out a heart transplant of a patient. Eli's vision makes him aware of the fact that his brother is keeping a secret that could be of great help for his case. Also, Eli finds out that his ex-fiancee slept with Matt.

After performing a dance act in the courtroom, Eli's capabilities of practicing law have come under scrutiny and he appears before State Bar of California for a hearing to determine whether he's fit to practice law. However, its Taylor who pleads to her dad, Jordan, to defend Eli's law license. Jordan agrees to represent Eli but another situation develops, Nathan has to decide whether he should protect his brother or shall tell the truth.

A teenage girl is expelled from school after playing George Michael's "I Want Your Sex" during the assembly. Jordan alongside Eli takes charge of the case, but Eli fails miserably in hiding his obsession for George Michael. Eli is motivated to go on date with Beth Keller, the girl with whom he had sex for the first time and who happens to know a big secret about Nathan. In the meantime, Taylor and Matt are working together on a case in which they are representing a judge suffering from cancer. They decide to sue the judge's son when he refuses to donate the bone marrow for his father.

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 gets a second attempt to make the case right which he previously won for a large motor vehicle by using questionable tactics. Meanwhile, Jordan introduces a couple of new associates added the W.P.K. named Taylor, who happens to be Jordan's daughter and Eli's ex-fiance, and Keith Bennett. Now Eli will have to deal with with ex-fiance in his office along with visions of him being in Hawaii. These impacts his case negatively due to his weird in the court.

After a pilgrimage to the Himalayas to scatter his dad's ashes and two weeks without visions, Eli has returned to work reinvigorated. Maggie, a first-year associate at W.P.K., suggests he take the case of a married couple from Mexico -- farmhands seeking compensation against a large produce manufacturer whose pesticide made the wife and her co-workers infertile. Eli resists taking the case until a singing boys' choir and a biplane his visions, returned persuade him otherwise. Unfortunately, his clients are keeping two secrets from him, challenging both their marriage and their American citizenship.

As Eli worries about his engagement party, he has a vision that lands him in the middle of a World War II battle, leading him to take the case of a National Guard Specialist who is suing her ex-husband for custody of their son. Meanwhile, Jordan requires Eli to provide proof that he's fit to work, so Eli enlists his brother in helping falsify medical records

Eli has a revelation when a man appears on his TV set and asks for help. The man turns out to be one of Nathan's patients who just awoke from a coma after five years to find his wife has taken over his company and has a new husband. He asks Eli to sue in order to get his life back on track.

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.