At police HQ, John arrives with a birthday present for Avery and has to empty his pockets at the metal-detector. Frank is leaving for the night and doesn't cut him a break, and the new security guard unwraps the present. John gets in and gives Avery his present – stress balls. Meanwhile the police bring in a corpse for Nance and she determines he has acute alcohol poisoning, and appears to recognize the corpse. After they leave, the "corpse" wakes up.
Nance comes in to tell Avery that they've found the corpse of Ken Rothman, who was fired three years ago for evidence tempering. They go to find the corpse but it's gone. John figures he used a drug to fake his own death and then bypassed the security cameras by taking a uniform and escaped into the air ducts. They determine Rothman made his way to the weapons lockers while the power goes down. Rothman makes an appearance with his men and takes everyone prisoner. They reveal they have plastic explosives and rig the station with it, and take the officers who come in prisoner as well as they arrive. One of Rothman's men sends a policeman out to tell Captain Ruiz he's holding the station hostage, and Rothman sends the civilians out.
While Rothman confronts Avery, All of the 14 officers are handcuffed to a wire shot into the wall but John manages to create a thermic reaction with a coffee pot and acid. Avery calls out to Captain Ruiz and relays Rothman's demand for a new investigation of his case. John burns through the wire and the officers try to make a break for it, but Rothman's men get them back under control. John has made his escape into the air vents.
Outside Ruiz and Frank arrive to secure the area while John looks on as Rothman punches Avery around. John manages to grab a phone and patch into the outside lines to contact Frank and give him an update. While Ruiz talks to Rothman, John has one of the TV newscaster cameramen patch into the station's security cameras where they see that Rothman has vials of smallpox.
The police outside evacuate the vicinity and call in the CDC while John catches Avery's attention and directs her to the stress balls he gave her earlier. She then drops them into the air vent where John uses them to make an electrified bolo and take out one of Rothman's men. He grabs some chemicals but loses one bottle, while Rothman worries at losing contact with his man.
The CDC show up and Captain Rockwell takes over the situation, demanding that John step down. Rothman figures out they're under surveillance while John rigs a gas bomb out of bleach, acid, and a light bulb. He knocks out another man then taunts Rothman over the walkie-talkie. Rothman goes to find him near the interrogation room but John has rigged the mirror from the room to distract Rothman and grab him. But Rothman reveals he's got a vial of smallpox and has inoculated himself and forces John to back down and untie the two captured men.
Rothman then calls Ruiz and demands the CDC truck to make his escape. Ruiz figures the CDC will take out the truck and the hostages rather then let the virus escape. Rothman leaves John and Avery handcuffed together and breaks a smallpox vial in the office before escaping. John manages to get the handcuffs open and then determines that the vial of smallpox is…vanilla extract. John figures that Rothman wants the smallpox vaccine the CDC will bring in, and he can create the virus from that.
Frank and Ruiz stop the truck and discover that Rothman decoyed them away while they grabbed the smallpox virus escaped in a separate service truck and they're heading for the docks to make their escape. At the ship, Rothman gets word the police are on the way but the police catch up to him and Avery puts him under arrest.
Later John still has trouble getting through the metal detector until he gives Brenda a hug for helping rescue her and the others. The entire staff give him a round of applause for helping to rescue them. John then meets with Avery to give her a new present – another set of stress balls to help her relax. She tells him to get out before giving them a try.