Lt. Van Buren listens to a complaint brought up by parents who have discovered their daughter in a topless photo on a blog called Fighter Boy. The detectives investigate, noticing that Fighter Boy blogs a lot about bombs, and has posted a video with a pipe bomb explosion. Lupo notices that the video also contains footage of propane tanks in the trunk of a car, and the car's license plate indicates that its registered in New York. Bernard and Lupo track down Fighter Boy, but he insists that he didn't make the video. He only found it and posted it because he thought it was cool. The detectives still need to find the real person who made that video, because the car bomb would be powerful enough to take out an entire city block.
Later, a scared Van Buren gets an MRI, and the scan should indicate a change in the degree of the cancer, and whether it has spread. The bomb video has been traced to a spot on Staten Island, and the detectives head over there. The police find the remnants of a pipe in the area, and mention that a pipe bomb was discovered in the restroom of a gas station a couple of weeks back. The bomb was old and rusty and probably a dud. Van Buren receives a call about getting a line of credit to pay her medical bills, with Lupo accidentally getting the gist of the call. Lupo talks to Bernard and suggests they throw a fundraiser for Van Buren, but Bernard doesn't think she'd go for that idea.
The bomb is traced to a couple of kids who also tracked down the place where the pipe bomb video was filmed. The found a piece of pipe and kept it for awhile, but finally ditched it in the gas station bathroom. One of the boys shows the detectives the website with the video, called Moot's Countdown. On the website is a blog entry which says that Moot is going to blow up a school.
The detectives decide to take the threat seriously, but they have no idea which school is being targeted. Skoda is trying to profile Moot, but is having a hard time since the blogger doesn't share too much personal information online. Lupo posts on Moot's forum, saying that he wants to do a copycat bomb in LA. Skoda thinks that Moot is a depressive, but seems less psychopathic than the Columbine shooters.
Meanwhile, Cutter and Rubirosa try to talk to a fed, as one of Moot's weapons (displayed on his site) has been traced to a gun dealer who stole Moot's carbine from a gun store.. The Fed blocks the attorneys' attempt to get to talk to the thief, saying that the federal crime outweighs a piddly state crime. ATF will not be too cooperative in helping them. And then Van Buren receives a call from her doctor. The first scan resulted in a lot of corrupted data, so she has to do the MRI over again.
Moot has figured out that the police are now reading his blog, so he says that he will now have to be more careful in what he reveals on his site. The detectives notice that Moot writes a lot about teachers on his blog. Maybe he's a disgruntled student who wants to get revenge? One teacher in particular got Moot's attention, a science teacher who seemed to be very religious and had been claimed to have branded crosses into his students' arms.
Lupo, Bernard and Rubirosa talk to a department of education rep, who claims that he can't discuss the specifics of the teacher's case. Rubirosa mentions that there is a credible bomb threat against a school, but the rep thinks that the teachers' union's lawyers would be an even greater threat. Someone else at the department of education clues the team in to a secret website where teachers can log in and complain about their jobs. She gives the detectives info on how to access the site, and maybe they can track down this particular teacher. Meanwhile, a very antsy Van Buren gets an MRI scan done for the second time.
Lupo finds what he needs from the secret website. The teacher is Ron Koslowski. The detectives track Ron down, and he says that the accusation was exaggerated. He was doing a scientific demonstration with a Tesla coil and ended up leaving marks on the students who willingly helped out with the coil. He doesn't recognize Moot, however. Ron was suspended for four months, but he decided not to stay in New York to teach. He took a lower paying job in an out of the way county, but at least he could still teach science to kids.
Cutter tries to get the grand jury to accept to subpoena the department of education so that they could get the case files open. They would have to open up the records of all the students at John Locke High school, but the jury refuses to give them the permission to go through the school records of minors.
Van Buren finds out that the rest of the team are planning a fundraiser for her, and she tells them that she doesn't want their pity, and that they should cancel the event. But Lupo isn't going to.
Using the teachers' website, the detectives match up identities to the teachers who are mentioned on Moot's blog. Most of the teachers can be found at a temporary reassignment center, or "Rubber Room". The Rubber Room is a place where teachers who have had complaints of misconduct or incompetence filed against them stay while their cases are investigated. Their union requires that every case gets looked at, so while the teachers are taken out of their classroom, they have to stay in the Rubber Room during regular school hours. It seems that many of the teachers are in the room because of exaggerated claims. A teacher who touched a student's hair was charged with assault. A teacher was reprimanded because he called a student a bastard, but that was after he was physically attacked by the student.
The detectives ask for the names of the problem students, but none of them match with Moot's names. Bernard starts to think that maybe Moot was a teacher who had to stay in a Rubber Room and had heard all these other stories of teachers being attacked by students. All of the teachers Moot mentions on his blog are in rubber rooms, except for a woman named Moira Scott. The detectives believe that Moot worked with Moira.
Moira and the lawyer supplied to her by her union meet with Cutter, but he's not able to get anything useful from her because of her lawyer. McCoy has watched the exchange and as Moira and her lawyer leave, he approaches her and pleads with her to talk to them. The lawyer strongarms McCoy, but McCoy gives him a piece of his mind. He argues that many innocent lives are threatened and Moira might know valuable information which would stop the massacre from happening. Moira finally speaks to Cutter. She explains that Moot is a teacher named Rick, who was great at his job but he couldn't handle the kids. A student who wanted a bathroom break ten minutes before class ended was told by Rick that he just had to wait. Instead, the student walked up to the front of the classroom and urinated in the trashcan. When Rick tried to stop him, the student accused him of trying to molest him. Rick was sent to a Rubber Room, but the charges were dropped. However, Rick's teaching career was already tainted by this incident, and his girlfriend decided to break up with him after that.
The detectives go to Rick's house but discover that he isn't there. Rick's parents explain that he had a substitute teaching job in Queens. In Rick's room, there is evidence of ammo and the ingredients needed to make a pipe bomb. The detectives identify the school and try to get it evacuated. Rick carried a backpack into the school. In the cafeteria, the detectives discover a bomb. Rick shoots at Lupo, saying that he has nothing to lose. But as he's distracted, Bernard sneaks up and disarms Rick.
At Van Buren's fundraiser, the detectives and attorneys celebrate the close of the case. Van Buren arrives, announcing that Frank is her fiance. She then receives a message on her phone, and she anxiously makes a call to her doctor. After the call ends, she whispers something in Frank's ear which makes him smile. Apparently, her cancer is in remission.