Malloy arrives at Vacaville, CA to meet with U.S. Marshal Vince Larkin who is supervising a separatee transfer to Carson City and then Mobile, AL. Malloy is described by Larkin's associate Skip Devers as a "real piece of work." Malloy is driving a luxurious convertible, decorated with the license plate designation "AZZ KIKR", and parks it in the handicapped spot. The three men meet with Malloy's partner Willie Sims, who is going undercover as a prisoner to meet with convicted drug lord Francisco Cindino. Malloy briefs them on the DEA's failure to acquire any useful information from Cindino, and the flight would be their last chance before Cindino is taken into FBI custody. Malloy is determined to not let the FBI get the glory of success.
When Sims is ordered to go aboard unarmed, Malloy initially counters the regulation, but reluctantly tells Sims to comply. He is then briefed on the other prisoners involved in the transfer, most of all Cyrus "The Virus" Grissom. Malloy feels insulted by Larkin's intellect and discussion of criminal behavior during incarceration. As Sims is taken aboard, Malloy conceals a gun in his sock. This act proves to be a fatal mistake for Sims later when the plane is hijacked by the prisoners and Sims is killed by Grissom, thinking he can retake the plane. When Malloy finds out about Sims' death, he furiously blames Larkin, calling his guards incompetent and summons military helicopters to Vacaville.
Malloy is present when Larkin contacts Grissom, the latter mocking Sims' weak attempt to retake the plane, and Malloy roars at Grissom, saying the electric chair would be more merciful than his supposed vengeance. While awaiting for the helicopers, Malloy is informed by Larkin of one Cameron Poe aboard, a former U.S. Army Ranger being released from prison after accidentally killing a drunk while protecting his pregnant wife, and that he informed Larkin of the plane's takeover in Carson City. Malloy refuses to believe Poe to be an ally and leaves with the arrived helicopters, vowing to shoot the plane down.
Unfortunately, the prisoners removed the plane's transponder and put it in a tourist plane flying to Arizona. Larkin informs Malloy that the Jailbird is flying to Lerner Airfield, but Malloy doesn't believe him. He is disgusted to notice normal civilians aboard the transponder's location and complains frequently during the flight to Lerner.
Upon arriving at Lerner, the prisoners' plans are foiled and are fleeing in the Jailbird, Malloy fires on Swamp Thing, hoping to stop them from taking off. He is shocked to see his car, having been stolen by Larkin, attached to the plane, only to crash through a tower and smashed to pieces right in front of Malloy. Enraged, he leaves with Larkin to chase after the plane.
Still vowing to shoot the plane down, Malloy orders the helicopters to fire, almost killing Grissom, but severely damaging the plane in the process. Poe contacts Malloy and Larkin, having retaken the plane. Malloy has a change of heart and reluctantly ceases attacking. The plane crashlands in Las Vegas where the prisoners are all killed or recaptured.
As Poe seeks out his arriving wife and daughter, Larkin apologizes to Malloy for stealing his car and suggests a bodyshop where it can be repaired. Malloy gently refuses, saying he was bored of the car, anyway, and that all worked out well.