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Several months after the events of The Fly, Veronica Quaife delivers Seth Brundle's child. After giving birth to a squirming larval sac, she dies from shock. The sac then splits open to reveal a seemingly normal baby boy. The child, named Martin Brundle, is raised by Anton Bartok, owner of Bartok Industries (the company which financed Brundle's teleportation experiments). Fully aware of the accident which genetically merged Seth Brundle with a housefly (a condition that Martin has inherited), Bartok plans to exploit the child's unique condition.
Martin grows up in a clinical environment, and is constantly subjected to studies and tests by scientists. His physical and mental maturity is highly accelerated, and he possesses a genius-level intellect, incredible reflexes, and no need for sleep. He knows he is aging faster than a normal human, but is unaware of the true cause, having been told his father died from the same rapid aging disease. As Martin grows, Bartok befriends him.
At age 3, Martin has the physique of a 10-year-old, and frequently sneaks around and explores the Bartok complex. He finds a room containing laboratory animals, and befriends a Golden Retriever. The next night, he brings the dog some of his dinner, only to find it missing. He enters an observation booth overlooking Bay 17. There, scientists have managed to reassemble Brundle's Telepods, but were unable to duplicate his programming that enabled them to teleport living subjects. Using the Golden Retriever as a test subject, the experiment fails, leaving the dog horribly deformed. The dog attacks and maims one of the scientists, horrifying young Martin.
Two years later, Martin's body has matured to that of a 25-year-old. On his fifth birthday, Bartok presents Martin with a bungalow on the Bartok facility's property. He also offers Martin a job: repair his father's Telepods. He apologizes about the Golden Retriever and assures Martin that its suffering was brief. When Martin is uneasy about the proposition, and Bartok shows him Veronica Quaife's videotapes, which documented Seth Brundle's progress with the Telepods. Seeing his late father describe how the Telepods ostensibly improved and energized his body, Martin accepts Bartok's proposal.
As he begins work on the Telepods, Martin befriends an employee, Beth Logan, and they grow closer. Beth invites Martin to a party at the specimens division, where he overhears some scientists and learns that the mutated Golden Retriever is still kept alive and studied. Thinking Beth is aware of the dog's imprisonment, Martin argues with her, leaves the party, and goes to the animal's holding pen. The deformed dog, in terrible pain, still remembers Martin, and he tearfully euthanizes it with chloroform. Martin reconciles with Beth, and rearrives at his father's "eureka" moment when he realizes the Telepod's computer need to be creative to analyze living flesh. Martin then shows Beth his perfected Telepods by teleporting a kitten without harm. They become lovers, but Martin begins showing signs of his eventual mutation into a human-fly hybrid. Martin devises a potential cure for his condition, which involves swapping out his mutated genes for healthy human genes. Martin shelves this idea when he realizes the other person would be subject to a grotesque genetic disfigurement.
Eventually, Martin learns that Bartok has hidden cameras in his bungalow, and has been lying to him for his entire life. Martin breaks into Bartok's records room, where he learns of his father's true fate. Bartok confronts Martin and explains that he's been waiting for his inevitable mutation. He reveals his plan to use Martin's body and the Telepods' potential for genetic manipulation for profit. Martin's dormant insect genes fully awakens, and his transformation into a human-insect hybrid begins. He escapes from Bartok Industries. Bartok is unable to use the Telepods, as it is locked by a password. Martin also installed a computer virus which will erase the Telepods' programming if the wrong "magic word" is entered. Bartok orders a search for Martin.
Martin goes to Beth, explains the situation, and the two flee. They visit Veronica Quaife's old confidant, Stathis Borans, who is now a reclusive, embittered drunk after her death. Borans confirms for Martin that the Telepods are his only chance for a cure. They keep running, but Martin's physical and emotional changes become too much for Beth to handle, and she eventually surrenders them both to Bartok. Without revealing the password, he becomes fully enveloped in a cocoon and enters the final stages of his transformation. Bartok interrogates Beth for the "magic word." Shortly after, the fully transformed "Martinfly" emerges from his cocoon and indiscriminately kills the scientists and security guards. A trace of his humanity remains, as shown when he doesn't harm a rottweiler and spares Beth when he encounters her during his rampage.
Martinfly breaks into Bay 17. He grabs Bartok and forces him to type in the password (revealed to be "DAD"). He then drags Bartok and himself into a Telepod. Martinfly gestures Beth to activate the gene-swapping sequence and, despite Bartok's protests, Beth complies. Martin is restored to a fully human form, while Bartok is transformed into a freakish monster that can barely crawl around.
The Bartok-creature is placed in a specimen pit similar to the one he had kept the mutated dog. In the final shot of the film, as it leans down to feed from a bowl, it notices a housefly.
For his entire life, Bartok has been lying about what?
hidden cameras