Benjamin Franklin Gates and Abigail Chase re-team with Riley Poole and, now armed with a stack of long-lost pages from John Wilkes Booth's diary, Ben must follow a clue left there to prove his ancestor's innocence in the assassination of Abraham Lincoln.

When vengeful General Francis X. Hummel seizes control of Alcatraz Island and threatens to launch missiles loaded with deadly chemical weapons into San Francisco, only a young FBI chemical weapons expert and notorious Federal prisoner have the stills to penetrate the impregnable island fortress and take him down.