Martin (Eric Stoltz) learns that he could eliminate the mutant genes in him through the TelePods if he brought in a host to teleport and swap genes with. Martin would have 100% healthy human genes while the host would suffer terrible physical deformities.
Martin also learns from his love interest Beth (Daphne Zuniga) that Bartok (Lee Richardson), the man he saw as his father, knows about them and their relationship after she is handed a videotape by the chief of security, Scorby (Gary Chalk), of the two having sex in his house, and when he checks out his house he finds that the lab installed hidden cameras everywhere to still keep watch of him. He goes to the surveillance room, where as he scans the tapes he finds one of his father Seth Brundle (Jeff Goldblum) during his transformation into BrundleFly. Bartok arrives and tells him that he was going to become like his father (but dubbed "MartinFly'), and that he was the pattern and the prototype for a whole new age of biological exploration. With him as the model and the TelePods as the tool, Bartok Industries would control the form and function of all life on Earth.
Martin manages to escape the lab and meet up with Beth, and together they evade the lab at every turn, including meeting with Stathis Borans (John Getz), who tells him that if he found a way to cure himself, he should use it. But, Martin's transformation into MartinFly gets increasingly worse, so Beth calls the lab back up and has them take Martin back. Martin goes into a pupal stage upon his return, and Beth is hosed down for contaminants and interrogated by Bartok for the password Martin knew that would activate the TelePods so he could use them.
Martin completes his transformation into MartinFly, and he goes and starts killing guards and scientists, including Scorby. Eventually, MartinFly gets a hold of Bartok, and using his hand types in "dad" as the password, starting up the gene swapping program, and he enters one of the TelePods with Bartok. MartinFly tells Beth to hit "Enter' on the keyboard to start the sequence, and she does. Martin comes out of the other TelePod a human again while Bartok is just a hideous creature. Martin and Beth kiss.
The last scene shows the deformed Bartok coming out of his cell in the Specimens Division into the observation area, and as he goes to take a drink from his food bowl, he sees a fly on the rim of it.
The end credits roll.
Thanks Tornado Dragon!