In 1974, Todd Bowden arrives at the doorstep of elderly German immigrant Arthur Denker, accusing him of being a wanted Nazi war criminal named Kurt Dussander. The old man initially denies the allegation, but eventually acknowledges his true identity. But rather than turning Dussander over to the proper authorities, Todd asks to hear highly detailed stories about his crimes, having recently become interested in the Holocaust. However, Todd still threatens Dussander with exposure should he refuse his demands. Over the next several months, Todd visits Dussander daily under the pretext of reading to him, all the while badgering him into revealing more details of his atrocities. Todd soon gives Dussander an SS Obersturmbannführer's uniform, forcing him to wear it and march on command.
As his relationship with Dussander continues, Todd also begins to have nightmares and sees his grades slip. After being confronted by his father about his grades, he forges his report cards before giving them to his parents. Eventually, Todd becomes in danger of flunking several courses. This causes Ed French, Todd's guidance counselor, to seek an appointment with the Bowdens. Todd and Dussander concoct a ruse, having Dussander go to French's appointment while posing as Todd's grandfather, Victor. Dussander falsely claims that Todd's grades are the result of problems at home, and promises to make sure his grades improve; French believes Dussander's story, but notices that Todd's "grandfather" does not mention him by name.
Knowing that Todd has been doctoring his report cards and knowingly socialized with a war criminal, Dussander blackmails Todd into spending his visits studying. With great effort, Todd is able to sufficiently improve his schoolwork. Since he no longer has any use for Dussander, Todd resolves to kill him and make it look like an accident. Todd had earlier claimed to have given a letter about Dussander to a friend; if anything should happen to Todd, the letter will be sent to the authorities. However, before Todd can kill Dussander, the old man claims to have written about Todd's involvement with him, and put his statement into a safe deposit box that will be found upon his death.
Over the next few months, Todd murders several homeless vagrants; he finds that committing murder somehow helps with his nightmares. As years pass, Todd's visits to Dussander become less frequent. He loses his virginity, but finds sex unsatisfying compared to the thrill of murdering local derelicts. When circumstances do not allow him to continue his serial killings, he picks a concealed spot overlooking the freeway and aims at people in passing cars with his hunting rifle. Dussander, suffering from his own nightmares, has also taken to killing the homeless for essentially the same reason as Todd, burying the bodies in his basement. Despite the link between them, Dussander and Todd are not immediately aware of each others' exploits.
One night, when Dussander is digging a grave for his latest victim, he has a heart attack. He summons Todd, who buries the body and cleans up the crime scene before finally calling an ambulance. At the hospital, Dussander happens to share a room with Morris Heisel, an elderly Jewish man who recognizes "Mr. Denker", but cannot place him. When Todd visits Dussander in the hospital, Dussander admits he was bluffing about the bank deposit box, as was Todd's threat about his letter. Dussander has read about the homeless men murdered by Todd, and tells the boy not to get careless. Dussander declares that "we are quits."
A few days later, Heisel realizes that Denker is Dussander, the commandant of the camp where his wife and daughters died in the gas chambers. An Israeli Nazi hunter named Weiskopf visits Dussander, telling him that he has been found out. After Weiskopf leaves, Dussander steals some drugs from the hospital dispensary and commits suicide. When Dussander's identity is revealed to the world, Todd convinces his parents that he didn't know about Dussander's past. Meanwhile a police detective named Richler, accompanied by Weiskopf, interviews Todd and is not so easily convinced. A vagrant recognizes Todd as the last person seen with several of the homeless victims, and notifies the police.
Meanwhile, French meets Todd's real grandfather. French brings up their previous conversation, but the real Victor Bowden obviously doesn't recall their meeting. French becomes suspicious and checks Todd's old report cards, finding that they have been tampered with. Later, he identifies the late Kurt Dussander as the man who met with him about Todd's grades. French confronts Todd, who responds by fatally shooting him. Todd then takes his rifle and ammunition to his hideout by the freeway. He embarks on a shooting spree, resulting in his death at the hands of the authorities five hours later.
- 1998 – Apt Pupil