After an assassin named Khamel kills two Supreme Court justices, Jensen and Rosenberg, Tulane University law student Darby Shaw writes a legal brief detailing her theory on why they were killed.

She gives the brief to her law professor/lover Thomas Callahan, who in turn gives a copy to his good friend Gavin Verheek, special counsel to the Director of the FBI. Soon after, a car bomb kills Callahan, but Darby avoids the same fate, because the drunk Callahan refused to let Darby drive his car.

Now realizing that her brief was accurate, she goes into hiding and reaches out to Verheek for assistance. An informant calling himself Garcia contacts Washington Herald reporter Gray Grantham with information about the assassinations, but disappears. Darby also contacts Grantham, who verifies her information as accurate.

Darby's computer, disks, and files disappear from her home. She is attacked at a hotel where she's hiding. She escapes the attack unharmed, but scared. She contacts and agrees to meet Verheek, but Khamel kills Verheek and impersonates him at the meet. Before Khamel can kill Darby, an unknown person shoots and kills him.

Darby agrees to meet Grantham in New York City, where she shares the theory expressed in her brief: the assassinations were done for oil tycoon Victor Mattiece, who intends to exploit the oil he found beneath Louisiana marshland that is habitat for an endangered sub-species of brown pelicans.

A court appeal to deny Mattiece the drilling rights is expected to reach the Supreme Court. Darby has surmised that Mattiece, hoping to turn the case in his favor, is behind the justices' murders; these two justices differ in their opinions on everything except protecting the environment.

As a generous contributor to the President, Mattiece expects that he would appoint justices that favor oil and gas exploitation over environmental issues while the next President may not do so. When Grantham tells her about Garcia, they discover that the man is Curtis Morgan, a lawyer in the oil and gas division at the Washington, D.C. law firm of White & Blazevich.

Darby visits the firm, pretending to have an appointment with Morgan, and is told that he had been killed in a mugging. Suspecting that his murder was related to the incriminating information, she and Grantham visit his widow, who eventually gives them a key to a safe deposit box. Darby visits the bank to retrieve the contents of the box.

After barely escaping death via car bomb, they reach the Washington Herald building, where they review the documents and a videotape recovered from Morgan's box. The tape corroborates Darby's theory, as Morgan's documents verify that Mattiece ordered the Justices to be assassinated.

With this evidence, Grantham writes his story. He gives the FBI a chance to comment and FBI Director Voyles confirms that Darby's "Pelican Brief" was delivered to the White House. He reveals the President ordered the FBI to "back off," and that the CIA is investigating Mattiece, with one of them killing Khamel to save Darby's life.

A plane that the FBI arranges for Darby flies her away to safety under the witness protection program. Sometime later, Darby is watching a TV interview of Grantham where it is revealed that Mattiece and four of his aides and lawyers have been indicted, the President's chief of staff Fletcher Coal has resigned, and the President (who received $4.2 million in contributions from Mattiece) is unlikely to run for reelection.

Grantham deflects speculation that Darby is fictional, but does agree that she is "almost" too good to be true, causing Darby to smile.