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.
Returning from the Himalayas, Eli goes back to work and Maggie Dekker, a first-year associate, gets him to take the case of a married couple who are illegals from Mexico and seeking compensation against a produce manufacturer whose pesticide made the wife and her co-workers infertile. Eli is reluctant until the he receives a visions of a boy's choir and a biplane. Unfortunately, it appears he's going to lose the case when he discovers the wife is lying. Meanwhile, Taylor tries to live with knowledge of Eli's aneurysm and inadvertently reveals its existence to Patti.
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.
"New Eli" gets to correct a case that "Old Eli" won via questionable methods for a motor vehicle manufacturer, but his odd behavior threatens the outcome. Meanwhile, Jordan entroduces two new associates -- his daughter, Taylor, who happens to be Eli's ex-fiance, and Keith Bennett.
Taylor convinces Jordan to represent Eli, whose antics in the courtroom have the State Bar of California questioning whether or not he's fit to practice law. Nathan finds his ethics tested when he must decide if it's better to support his brother, or to be honest.
Eli is reduced to playing second fiddle to Maggie as she works on a malpractice suit against a doctor from Nathan's hospital. Meanwhile, Taylor believes a musical performance by singer George Michael can help her reconcile with Eli. Meanwhile, Matt and Keith argue over how to handle the Turk case.
A real estate mogul's desire to create a shopping mall by evicting a whole neighborhood, makes for an interesting case as Eli defends him after foreseeing an earthquake's epicenter in that area.
George Michael seeks representation by Eli on behalf of a teenage girl who has been dismissed from school after playing one of his songs with suggestive lyrics during an assembly for abstinence-education. Meanwhile, Eli prepares for his first date since his engagement broke off, and Taylor and Matt work together on a judge's lawsuit.
Eli has visions of the day that his father died while defending Nathan in a malpractice suit. Meanwhile, Taylor takes on the divorce case of a man who is accused of cheating... on his own wife, using an anonymous Internet chat ID.
Eli takes on the case of a prisoner who is Keith Barnett's ex-client. Meanwhile, one of the law firm's partners, Marci Klein, shows up to see why Jordan is losing so many of the firm's Fortune 500 clients.
Eli has another vision of an earthquake and goes to court to get the city to shut down the Golden Gate Bridge. Marci Klein appoints Maggie as second chair as she tries to shut down Eli's case, and uses his efforts as ammunition to ouster Jordan from the firm.
Eli undergoes surgery for his aneurysm, but when complications arise his brother Nathan must make a difficult decision.
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 and finds that it 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, Matt, Taylor, and Maggie all find themselves in the small town of Sonoma, working on the same case from different sides... and dealing with the issues between them. Meanwhile, Jordan asks Patti to a charity dinner, and Nathan learns what Frank has been hiding.
Eli and Maggie deal with the aftermath of the change in their relationship while dealing with the Bay West case. Meanwhile, Jordan tries tor resolve matters with Jordan and reveals how important winning the case is, and a new man enters Maggie's life.
Eli and Jordan represent 300 employees in a class action against a greedy CEO whose bad decisions cost hundreds their jobs. Meanwhile, Jordan and Posner compete for an award, Matt joins Wethersby & Stone, and Maggie gets a glimpse of the real Paul Rollins.
Eli has a vision which leads him to believe that one of the Wethersby-Stone staff members will die in a plane crash. Meanwhile, he and Keith try to save a woman who has been denied a heart transplant because the donor's parents disagree with her religious beliefs.