Eli Stone is a rising, successful attorney. Not only is he working for Jordan Wethersby's renowned law firm, but he is engaged to Jordan's daughter Taylor, also an attorney. However, Eli begins having hallucinations (many of which involve singer George Michael) that may either be linked to a medical condition, or the bizarre chance that he is a modern-day prophet. The hallucinations lead him to reluctantly take a case involving his college friend/first lover, Beth Keller. Beth's son developed autism, which Beth blames on a childhood vaccine produced by a major pharmaceutical company. At the same time, Eli's behavior about his visions makes him recall his estranged relationship with his now-deceased father, whom Eli believes was an alcoholic.

After two weeks without the visions, Eli hesitates to take the case of a Mexican couple suing a produce conglomerate for their use of pesticides, believing he has no chance of winning. However, he begins to doubt the odds after his visions prove more truthful than before.

As Eli struggles to come to terms with the end of his engagement to Taylor, his visions convince him to help a former coma patient who wants to get his life back. Meanwhile, Jordan defends an old friend in a discrimination lawsuit against another of the same ethnicity.

Eli gets an opportunity to make things right when he revisits an old case that he unscrupulously won for an automaker, but his efforts could be undone by a series of courtroom hallucinations. Meanwhile, Jordan welcomes two new lawyers to the firm, one of whom he had fought against in the previous episode.

Eli needs Jordan's help when he is in danger of being disbarred, after an embarrassing courtroom episode puts his ability to practice under scrutiny. However, Eli's fate may ultimately rest with Nathan's testimony about his brother's condition---and Eli's own conscience.

Eli's bar hearing admission may saved his law license but compelled Jordan to reduce him in stature at the firm. It places him in the unfamiliar position of playing second fiddle to the inexperienced Maggie. The two are involved in a malpractice suit against an anesthesiologist who used to work at Nathan's hospital but was fired after a botched anesthesia that led to the death of the teenage plaintiff's mother during heart surgery.

Eli's defense of a real estate mogul takes an interesting turn when his client's desire to evict residents from their homes (in an area where he wants to build a shopping mall) may be the only way to save them from an earthquake Eli has foreseen.

Eli's occasional visionary muse, George Michael, seeks his counsel in person on behalf of a teenage girl who was expelled from school for playing a suggestively titled song of Michael's during an abstinence education assembly. Jordan, who is heading the case, begins to display an unusual upbeat side, leading Eli to believe his senior partner is a fan of George Michael's music. Meanwhile, Nathan has found a neurosurgeon to help his brother, but is unwilling to make the choice that could decide Eli's fate.

Eli's visions bring him back to the supposed earthquake. This time, he sues San Francisco to close the Golden Gate Bridge. Supported by a so-called quack scientist, Eli opposes Ms. Klein and Maggie in a court case that could decide the lives of hundreds. At the same time, Ms. Klein uses Jordan's apparent lack of control over Eli as ammunition to remove Jordan as managing partner. At the end of the episode, the earthquake does hit and destroys the Golden Gate Bridge. Fortunately, because the bridge was closed (they managed to persuade San Francisco to close it), no one was killed on it when it collapsed. Ms. Klein reconciles and keeps Jordan as managing partner.

Eli takes a case involving a man's right to die; the case is intertwined with the aftermath of Eli's surgery to remove his brain aneurysm, which forces Nathan to decide whether to remove Eli from life support. Eli apparently comes face to face with God . . . who bears an uncanny resemblance to George Michael.

Eli is free from his visions for the past six months after having an operation to remove his brain aneurysm—or so he thinks. Nate experiences visions of his own suffering a similar fate as Eli that go along with the gift. Taylor faces a dilemma when her father is trapped in a collapsed building.

Eli has his vision back with a beautiful brunette singing to him. The lady is Grace who turns out to be very much real and not just a vision after meeting her. Eli and Grace fall for each other. The same week Eli represents a father attempting to stop his son from receiving a military burial.

Eli and Jordan have problems with regular clientele and keeping up with costs with their new firm. Eli convinces Jim Cooper, a billionaire philanthropist, to lead the case on trial drug testing. Eli is put in a difficult situation when he learns Cooper's son wants no part in the trial. Meanwhile, Keith represents Patti's daughter. while Matt and Maggie work to find the traitor amongst their midst.

Patti's daughter is arrested for drug abuse. Eli is convinced that her daughter's innocent after his most recent vision. A guest performance by Seal.^[16]

Eli finds out more about Nate and Beth's engagement being called off. Keith and Eli help a minister with a lawsuit against his own church, and Taylor and Matt find out about their baby's health.

When a news anchor from one of the biggest media corporations loses his job, Eli, Taylor, Matt and Maggie share an awkward car ride to Sonoma to question a witness---and a more awkward presence before a judge whom Matt dated in law school but broke up with by e-mail after graduation. Meanwhile, Eli is now suffering the consequences of the 'Dark Truth' treatment, plagued with not one but two brain aneurysms.

Eli's latest visions lead him to believe someone close to him will die in a plane crash. As Eli tries to unravel the mystery, he and Keith take on the case of a woman who is in need of a heart transplant--but whose donor's parents have reversed their consent over the woman's atheism. Little does Eli know that the heart he is fighting for will take on greater significance after he prevails and the woman goes into transplant surgery.