Tulane University Law School student Darby Shaw (Julia Roberts) theorizes that there may be some similarity in their otherwise-different voting patterns that may provide a motive for their assassinations. She decides to research the two justices' records and cases pending before the Court, suspecting the real motive might be simple greed, not politics. She discovers that both were protective of the environment in their votes. She writes her theories into a legal brief, which she shows to her law professor, mentor and lover Thomas Callahan (Sam Shepard ). Callahan, a recovering alcoholic, is grieving for Rosenberg, whom he interned for. He finds Darby's work interesting, but fails to recognize the high stakes involved. Nevertheless, he gives a copy of the paper (which known becomes as the "Pelican Brief") to Gavin Verheek (John Heard), a friend of his who works as a lawyer with the FBI.
Not long after this, Callahan is killed by a car bomb as the couple is leaving a bar in New Orleans; Darby escapes the attack because she holds back from getting into the car with her drunk lover. She soon realizes she is under surveillance, and is subsequently attacked by an unknown assailant. Realizing that her brief was accurate, she goes into hiding and reaches out cautiously to Verheek for help.
Meanwhile, in Washington, DC, political reporter Gray Grantham (Denzel Washington) is contacted by an anonymous informant who calls himself "Garcia" and claims to have information about the assassinations which he had apparently seen inadvertently at his place of employment. Grantham manages to take a photograph of "Garcia" but is unable to identify him. "Garcia" subsequently disappears. Darby then makes contact by telephone with Grantham and mentions the Pelican Brief; although initially skeptical, Grantham discovers that the limited information Darby discloses has validity.
Darby finds out from fellow classmate Alice (Cynthia Nixon) that her apartment has been ransacked and her computer, disks and files are gone. Soon after, the man who had attacked her previously finds her again and gives chase, but Darby evades him a second time. She contacts Verheek and arranges to meet him the next day in a crowded public place. Prior to their meeting, Verheek is murdered in his hotel room by Khamel, who then goes to meet Darby dressed as Verheek. Just before Khamel can kill her , however, he is shot and killed by an unknown agent, and Darby flees.
Darby contacts Grantham again and agrees to meet him in New York City. There, she gives him the details of her brief.
The legal brief speculates that the assassinations were committed on behalf of Victor Mattiece, an oil tycoon who wants to drill for oil on a Louisiana marshland which is a major habitat of an endangered species of pelicans. A court case on appeal, filed on his behalf to gain access to the land, is expected to make its way to the Supreme Court. The two slain justices had a history of environmentalism — their only common view — and thus Darby surmised that Mattiece, who has a pre-existing business relationship with the President, hoped to turn the case in his favor by eliminating the two justices, thus leaving his friend, the President, in a position to appoint new justices more likely to rule in his favor.
Grantham tells her about "Garcia", and together they discover that "Garcia" is Curtis Morgan (Jake Weber), a lawyer in the oil and gas division of White & Blazevich in Washington.
Darby visits White & Blazevich, pretending to have an appointment with Curtis Morgan. When she is told that Morgan had been killed by muggers just a week ago, she suspects that his discovery of incriminating evidence was the real reason for his murder, and Darby hurries out of the office. She and Grantham visit his widow , who gives them a key to a safe deposit box he owned.
While Darby visits the bank to retrieve the contents of the box, she is followed and a bomb is planted in her car. When she and Grantham return to their vehicle, Grantham has difficulty starting the car, and Darby recognizes the faltering sound as what she heard just before Callahan was killed. She stops him and they flee the vehicle. They are instantly pursued on foot and by a car, which finally crashes into their parked vehicle, detonating the bomb and killing one of their pursuers.
They escape to the Washington Herald building, where they review the documents and a videotape from Morgan's box. The tape contains testimony from Morgan that confirms his discovery that Mattiece ordered the assassination of the Justices and the documents are memos that confirm these accusations. With the evidence that he needs, Grantham writes his story. He gives the FBI a chance to comment, and Director Voyles (James B. Sikking) comes to meet with him personally. On the record, Voyles confirms that the Pelican Brief was delivered to the White House; off the record, he reveals that the President ordered the FBI to "back off". He tells Darby that CIA agents were investigating Mattiece, and that one of them killed Khamel to save her life. Voyles arranges for a plane to fly Darby , accompanied by Grantham,to an undisclosed foreign location. Upon arrival, they are given a copy of the day's Herald with their story, which credits both Grantham and Darby in the byline. After embracing, Darby departs in a waiting van and Grantham returns to the plane.
The movie ends with Darby in her foreign hideaway, watching Grantham being interviewed on TV, where it is revealed that Mattiece and two of his lawyers have been indicted in federal court, the President's chief of staff has resigned, and the President himself will not run for office again. Grantham deflects speculation that Darby is fictional, a composite of sources, but does agree that she is "almost" too good to be true. Her life having been saved, Darby smiles as the screen cuts to black.
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