John Kruger, code name: "Eraser", is a U.S. Marshal who works for the Federal Wittnes security program (WITSEC). John is assigned to protect Lee Cullen, a senior executive for Cyrez Corporation, a company that creates and manufactures weapons for the military. Lee has come across plans in which Cyrez plans to sell a top secret electronic pulse rifle to terrorist Sergei Ivanovich Petrofsky. With its unparalleled firepower, the sale of such weapons to the wrong hands would tip the balance of power. To procure evidence, Lee copies critical data onto two discs: one for the FBI, the other as evidence in order to publicize Cyrez's transgressions. However, William Donahue, the CEO of Cyrez, catches wind of Lee's intentions and orders her into his office. Donahue commits suicide to escape punishment, and Lee barely escapes from Cyrez. Disappointed with the FBI because of failure to guarantee her safety, she delivers the evidence but refuses to submit herself to WITSEC, despite John's advice.
The same night, Lee is targeted for assassination by a group wielding a couple of the aforementioned pulse rifles. John rescues Lee and takes her to New York City to hide her. However, soon afterwards John learns from his mentor, fellow marshal Robert DeGuerin, that someone, perhaps a mole within the WITSEC, is targeting witnesses in top-level cases, including Lee. They proceed to the location of one of the targeted witnesses, but DeGuerin kills the witness personally, revealing himself as Donahue's U.S. Marshal mole and the leader in the scam, which includes even Undersecretary of Defense Daniel Harper. In order to facilitate his plans, DeGuerin tries to frame John as the mole, but John escapes and rescues Lee in the nick of time.
Since the evidence against Cyrez has fallen into the hands of the enemy, John, Lee and Johnny Casteleone, a mob witness whose life John once saved, penetrate the main office to read Lee's copy, since the data on the disc is encoded for Cyrez computers only. They are discovered, however; DeGuerin kidnaps Lee and has her brought to the Baltimore docks where a railgun shipment is being loaded onto a terrorist freighter. With the aid of Johnny, his cousin Tony Two-Toes and two associates, John rescues Lee and prevents the railgun shipment.
After a hearing for DeGuerin and his fellow conspirators a few weeks later, and with the implication that under civil law jurisdiction a conviction and sentence of the culprits will not be possible, John publicly fakes his and Lee's death, but subsequently eliminates DeGuerin and the conspirators "erasing" them throughly in an arranged train accident.