Many lawyers consider themselves prophets, but Eli Stone may be the real deal. Eli has built a successful career at a top law firm in San Francisco representing only the biggest and richest corporations that make a habit of screwing over the little guy. But after experiencing a series of odd hallucinations, Eli seeks to find a deeper meaning to life while trying not to lose his job and destroy his relationship with the bosses' daughter. When Eli discovers an aneurysm in his brain, he wonders if his condition is truly medical or if perhaps he now has a higher calling.
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.
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.
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 and Jordan take on a case to force the government to allow clinical trials of marijuana to cure MS. However, the billionaire philanthropist who backs them soon realizes that his own soon, suffering from MS, doesn't wish to participate. Meanwhile, Maggie and Matt try to determine who the mole is within the new firm that is luring clients to Posner/Kline.
Eli has visions from his father's point of view of Nathan's 12th birthday. Meanwhile, Taylor has news for Matt about her pregnancy, and Keith suspects Patti's daughter of using drugs.
Keith begins to doubt Angela's innocence, but Eli's vision leads him to believe she's innocent. When he understands what the vision truly means, he and Patti come to a turning point in their relationship. Meanwhile, Frank sets up Eli on a blind date, and Maggie gives advice to Matt on Taylor's pregnancy.
While representing a Nobel Prize winner destined to find the secret of cold fusion in the future, Eli undergoes a dangerous procedure with Chen's rival acupuncturist to see if he has a future with Ashley Cardiff. Meanwhile, Taylor learns more than she wants to about her father while representing him in his divorce.
When Nathan asks Eli to be the minister at his wedding, Eli is forced to turn to Frank's rival to undergo the "Dark Truth" ritual and learn what his visions mean. Meanwhile, Taylor and Matt get unwanted news about their unborn child, and Keith and Eli defend a minister in a discrimination case.
Eli, Maggie, Matt, and Taylor all end up working in the same case, in a small town called Sonoma. Eli and Maggie get much more close, but they end up having an argument.
While handling the Sonoma case, Eli and Maggie deal with the change in their relationship and Maggie meets a new man.
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.
After seeing a vision of a plane crash, Eli is convinced that one of his friends will die in a plane crash. British actress Jaime Murray and Gregory Smith co-star.