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.

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 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 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.

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.

A non-profit attorney has a mysterious fate that leads her to Eli... and the two become romantically involved. Meanwhile, Eli and Julie take on the case of a father who wishes to prevent his dead son from being buried with military honors.

In the aftermath of Posner/Klein's departure, Eli tries to keep Matt with the firm by offering him a pro bono case concerning Homeland Security, and has a vision concerning Maggie's upcoming wedding.

Eli starts to get envious of Maggie going out with Paul, especially since Paul works at Posner & Klein, where Maggie works. Meanwhile, Eli fights for the little man against a greedy CEO whose bad decisions cost hundreds of jobs.