Dr. John Mathewson (John Lithgow) discovers a new process for refining plutonium to purities greater than 99.997 percent. The United States government provides him a laboratory located in Ithaca, New York, masked as a medical company. John moves to Ithaca and meets real estate agent Elizabeth Stephens (Jill Eikenberry) while searching for an apartment. He attempts to win the affections of the single mother by inviting her teenage son Paul (Christopher Collet) to take a tour of the lab.
John is confident in the lab's cover story but Paul, an unusually gifted student with a passion for science, becomes suspicious when he discovers a statistically impossible patch of five-leaf clover on the grounds. Paul and his aspiring journalist girlfriend, Jenny Anderman (Cynthia Nixon), decide to expose the weapons factory in dramatic fashion. Paul breaks into the lab and steals a container of plutonium. To obtain maximum publicity, Paul decides to build an atomic bomb and enter it into the New York Science Fair. After convincing his mother and his school that his project is about hamsters bred in darkness, he begins research and construction of the nuclear device.
The lab discovers that a container of plutonium has been replaced by a bottle of shampoo mixed with glitter. A military investigation team, led by Lt. Colonel Conroy (John Mahoney), arrives on the scene and determines that Paul is responsible for stealing the plutonium. Suspecting him of terrorist intent, the investigators search Paul's home and discover that he and Jenny have left for the science fair.
After the agents capture the couple in New York City, John, who feels personally responsible for the crisis, has a private talk with Paul and convinces him to give the bomb to the agents before a group of other participants at the science fair help Paul and Jenny escape from the hotel.
In an effort to expose the lab, Paul hatches a plan to return the bomb on his own terms. Ensuring Jenny is a safe distance away, he calls the agents from a pay phone and walks into the lab with the bomb while being surrounded by snipers and agents. During the standoff, negotiations stall and Paul arms the bomb. John, convinced that Paul is not an actual terrorist, attempts to intercede on his behalf.
Due to radiation from the plutonium, the bomb's timer suddenly activates on its own and begins to count down with increasing speed. Paul suggests taking the bomb to a quarry outside of the town, but John advises against it, telling Paul that the bomb is much more powerful than he believed. Desperate to defuse the bomb, all sides put down their weapons and frantically work as a team to dismantle it. They manage to disarm the bomb before it explodes. After a brief moment of relief, Conroy decides to arrest Paul. John refuses to cooperate and opens the door to the lab, revealing a large crowd, including Jenny and the press. The film ends as John, Paul, Jenny and Elizabeth all depart the scene.Christopher Collet as Paul Stephens
John Lithgow as John Mathewson
John Mahoney as Lt. Col. Conroy
Jill Eikenberry as Elizabeth Stephens
Cynthia Nixon as Jenny Anderman
Robert Sean Leonard as Max (as Robert Leonard)
Richard Jenkins as Radiation Controls Officer
Gregg Edelman as Science Teacher
The plot was likely influenced by the case of John Aristotle Phillips, a Princeton University undergraduate, who came to prominence in 1977 as the "A-Bomb Kid" for designing a nuclear weapon in a term paper using publicly available books and articles.
$13 million of the budget - the actual cost of making the movie - was provided by Thorn-EMI Screen Entertainment. The rest of the budget consisted of consultancy fees for Gladden.
The Manhattan Project was filmed in and around Rockland County, New York. Locations included Suffern High School, King's Daughters Library in Haverstraw and the Orchards of Conklin in Pomona. The producers held an actual science fair at the New York Penta Hotel in which participants received $75, and utilized the set for filming. The nuclear sets and effects were designed collaboratively by the production designer Philip Rosenberg, and Bran Ferren who is credited with the special effects. Ferren used literally tons of technical gear purchased surplus from Los Alamos National Laboratories, and performed most of the visual effects work, including robotics, live on set.
The film's director and screenplay co-writer Marshall Brickman had established his career as a co-writer on several Woody Allen films. The Manhattan Project was his third film as director, following the comedies Simon (1980) and Lovesick (1983).
The film earned $2 million in film rentals to theaters in the United States during its first year of release.
Chicago Sun-Times critic Roger Ebert gave the film four out of four stars and called it "a clever, funny and very skillful thriller ... that stays as close as possible to the everyday lives of convincing people, so that the movie's frightening aspects are convincing". He particularly took note of how "sophisticated" the film was about the relationship between Paul Stephens and John Matthewson, while praising Brickman's ability to "combines everyday personality conflicts with a funny, oddball style of seeing things, and wrap up the whole package into a tense and effective thriller. It's not often that one movie contains so many different kinds of pleasures."
Brickman received the President's Award from the Academy of Science Fiction, Fantasy & Horror Films for The Manhattan Project. Brickman would not direct again until the 2001 Showtime television movie Sister Mary Explains It All. In the role of Jenny, Cynthia Nixon was nominated for the Young Artist Award in the category of Exceptional Performance by a Young Actress, Supporting Role.