The Order 23 Job begins in a courtroom, where a jerk of a defendant is being sentenced for stealing the life savings of dozens of people. He is given an eighteen months sentence because he is serving as a federal witness with the US Marshals. The full courtroom is very angry at the sentence and a man named Ronald pulls a gun on the defendant, only to be stopped from committing murder by Nate. However, before Nate can talk to him, Ronald slugs the defendant, identified as Eddie Maranjian.
Nate tells Ronald that he is there to help Eddie's clients, and Hardison explains that they're trying to find the $400,000 that Eddie liquidated right before his trial. Nate says that Eddie doesn't deserve to be killed. Ronald tells them about his sister, who died because she didn't have money to pay for a hospital; Eddie had stolen all of her savings.
Hardison discovers that the jail Eddie's going to is more like a country club, and Sophie points out that if Eddie isn't afraid of prison, he has no reason to tell them where the money is. Nate discovers that Eddie is afraid of disease and germs.
Meanwhile, Eddie makes conversation with the US Marshals protecting him. He tells the Marshals that the way he stole the money wasn't by gaining the clients' trust, but by making the clients' fear of losing money stronger than their distrust of him. Parker sneaks around in a vent and manages to drug Eddie's drink, scaring him by pretending to be a rat. When Eddie drinks the drugged liquid, he faints.
The Marshals call over a nearby doctor (Nate) from jury duty. Nate says that Eddie may have a concussion from Ronald's punch in the courtroom and decides he needs an MRI. The Marshals take Eddie to the hospital, which the team is ready to steal.
Th team congregates on the eighth floor, which is empty because it's only used for storage. Parker 'acquires' medical supplies and poses as a nurse, while Hardison sets up speakers all over the eighth floor. Nate is pretending to be a doctor and Eliot and Hardison are posing as local cops. Parker takes Eddie to the MRI room and gets the Marshals to remove his handcuffs. Eliot notices a kid who's being brought to the hospital for what is apparently not the first time. The boy's father tells a nurse that the boy fell off his skateboard.
Nate sends Eddie to the eighth floor, citing the rash that Parker gave the man using a spray. Hardison and Eliot make friends with the Marshals; meanwhile Eddie is being handcuffed to a hospital bed and introduced to Sophie's slightly crazy New York persona. Nate has Parker make announcements over the PA system that he tells her are intended to suggest symptoms to Eddie's amygdala, making him scared. Eddie is made suspicious when a 'Special Health Warning' is on the television, only to be interrupted by static. Nate plays prerecorded sound bytes about health warnings and escaped contagions to scare Eddie; it seems to be working.
A real patient needing the MRI tips off the Marshals that Eddie is gone. Bob, one of the Marshals, is going to call it in, but Eliot convinces him that it would damage their careers if it gets out that they lost a prisoner. Sophie's itching symptoms, now being copied by Eddie, get worse and she goes into cardiac arrest after her nose starts bleeding. Nate, Parker, and Eliot (now dressed as an orderly) try to save Sophie, but she 'dies' within Eddie's view. Eddie frantically asks what's going on, but the team ignores him and he becomes even more afraid.
The Marshals check video of the hospital's exits, but surmise that Eddie is still in the building. Hardison suggests that Eddie is trying to lure the Marshals out of the hospital. Bob tells Hardison to tell Eliot to search the hospital with the other Marshal, Charlie. Hardison relays the message while going to search the Marshal's cars on Eliot's suggestion. Eliot (back as a police officer) is on his way to start searching with Charlie when he sees the young boy again, getting a cast put on his broken arm. Eddie, meanwhile, is freaking out to the point where his nose actually starts bleeding.
Eliot takes out his com and talks to the boy's father in a stairway. Eliot confronts the father on the boy's condition. He points out bruises on the boy which date to three days and seven days before. Eliot holds the father over the edge of the railing, scaring the man thoroughly as he steals his driver's license. He tells the man that he's watching him now. The father tells Eliot that he's better than some men who never even see their kids.
A hospital security guard makes his way to the eighth floor and almost finds Eddie, but is ordered to stay in a shower by Sophie dressing in biohazard gear. Hardison searches Charlie's car and finds very suspicious materials. Charlie, meanwhile, discovers that Eliot and Hardison aren't real cops. Hardison tries to tell Eliot that Charlie's a hitman for the Armenian mob, who Eddie also stole from, but Eliot still hasn't put his com back in. Eliot begins to search the morgue with Charlie, while the hitman gets ready to shoot Eliot in the back. Eliot is alerted at the last moment by Hardison's version of a warning: a Star Trek reference over the PA system. Eliot just manages to dodge several bullets. This starts an awesome fight scene, which ends when Charlie is knocked unconscious.
Eddie is, at this point, horrified by the sounds of monitors, dying patients and shouting doctors from Hardison's speakers. Nate tells him that the Marburg virus has been weaponised and that they have seen a dozen cases, before passing out. Eliot stores Charlie in a drawer on top of a dead body. He gets the beginning of a lecture from Hardison about taking out his com, but the hacker notices that Bob, the real Marshal, is headed up to the eighth floor.
Parker handcuffs Nate to a hospital bed, telling him that an Order 23 is in effect. Eddie guesses that an Order 23 means to leave them in the room. When Parker's about to leave Nate and Eddie in the hospital room, Eddie offers her $400,000 to get him out of there, now. Parker ignores Nate's warnings of an epidemic and leads Eddie down the hall. Nate easily escapes the cuffs, and Eddie manages to steal a taser from the discarded biohazard gear. Bob finds Eddie's tie in the hospital room and calls the police. Eliot tells Randy, the young boy, that he could talk to one of the police officers about what happened to his arm. Randy says that the cops are friends and drinking buddies with his father and he can't tell them. Hardison comes to get Eliot and the two leave, despite the fact that Eliot obviously still wants to help Randy.
Parker and Eddie have almost made it to the exit. Parker warns Eddie of a camera they have to avoid, and he tasers her and leaves by himself. Eddie manages to steal a car and drives to the courthouse. He breaks in and retrieves a bag from the janitor's closet, only to be stopped by the whole team as he tries to leave. Eddie tells the team that they're going to jail for years for kidnapping and assault, among other things, while he will only serve eighteen months. Eddie runs out of the courthouse, only to be arrested by several cops. He tells them about the criminals who are inside, but is totally ignored by the officers, who say he is under arrest for assaulting a security guard (the man who was stuck in the shower saw Eddie as he escaped with Parker), tasering a nurse (Eddie tasering Parker was caught on another camera) and escaping federal custody. Eddie is loaded into the back of a police car as the team watches from the courthouse.
Hardison and Eliot show Bob where the Armenian hitman was stashed, and Eliot tells Bob that the Marshal will get the credit for the man's arrest. Bob asks Eliot how he can thank him and Eliot gives Bob the abusive father's license. Bob goes to the boy's house and identifies himself as a US Marshal. He takes Randy from the house while Eliot watches from his car across the street.