The story begins with the assassination of two philosophically divergent Supreme Court Justices. Liberal Justice Rosenberg is killed at his home, while the conservative Justice Jenson is killed inside a porn theatre. The circumstances surrounding their deaths, as well as the deaths themselves, shock and confuse a politically divided nation.
While the public speculates about who may have killed them and why, the main character, Darby Shaw, a Tulane University Law School student, decides to research the two justices' records and cases pending before the Court, suspecting the real motive might be simple greed, not politics. She writes a legal brief speculating that the assassinations were committed on behalf of Victor Mattiece, an oil tycoon wanting to drill for oil on Louisiana swamp land which is a major habitat of an endangered breed 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 surmises that Mattiece, who has a pre-existing business relationship with the President, hoped to turn the case in his favor by eliminating two justices, thus leaving his friend the President in a position to appoint new justices more likely to rule in his favor.
Darby shows the brief, which becomes known as the 'Pelican Brief' to her law professor/mentor/lover, Thomas Callahan, who shows it to his Washington-based friend, Gavin Verheek, a lawyer working for the FBI. Both men are killed soon after.
Afraid that she will become the next target, Darby goes on the run. Eventually, she contacts the Washington Post reporter Gray Grantham, and the two set out to prove her brief correct.
The various parties quickly take sides. The President and his Chief of Staff try to cover up his connection to Mattiece, which would be politically damaging. The FBI wants to bring in Darby to protect her and to verify her story. Allies of Mattiece try to kill her to make sure the cover-up holds.
Eventually, every piece of the story is in place. Grantham obtains videotaped testimony from a pseudonymous lawyer named "Garcia", as well as a document that points to involvement by Garcia's law firm which worked for Mattiece. With this evidence, Grantham and Darby approach the Post chief editor. The story appears in the next edition with front page photographs of Fletcher Coal (the aforementioned Chief of Staff), Mattiece, etc. FBI chief Denton Voyles is ecstatic and shows up at Coal's residence early in the morning to confront him.
Darby crisscrosses the country, then reaches an island in the Caribbean Sea, where Grantham eventually joins her.
