The movie opens at a hospital where Peter, a doctor who works for the CDC, is convincing Susan, a scientist to use a genetically modified organism to kill the cockroaches which are spreading Stricklers disease, which is an epidemic that has been affecting kids within New York City for 2 years. Moved by the infection and near-death state of the kids, she chooses to make a cockroach killing bug called the Judas Breed. When engineering the organism, she ensures that they could not reproduce within the lab and believes that they will live for one generation then die out. After releasing the Judas breed the epidemic is eradicated, and Susan and Peter fall in love and get married. After they do so, 3 years pass, with nothing unordinary happening.

However, after the murder of a corrupt preacher, and a mysterious bug found by two kids it is discovered that the Judas breed are still alive, and shortly afterwards the Judases kill the kids who discovered the bug, and abduct a small boy named Chuy. This causes Susan, Peter, and a cop named Leonard to enter the tunnels, and Chuy’s father, Manny, to separately do so. Whilst they are in the tunnels, Susan uses her knowledge of insects to realize that there is only one fertile male Judas. However, shortly afterwards Manny and Leonard are murdered by the Judases, but before Manny dies, he is able to find Chuy and leads Susan to him. After the deaths of Manny and Leonard. In order to let Chuy and Susan escape, peter sends them up a small hand pulled lift, however he stays behind and runs into a breeding room for the Judas. Seeing that the room is lined with gas pipes he chooses to break some, and then create a spark, whilst jumping into water as soon as it ignited. This creates a large explosion which kills all of the Judas except the male. 

After the explosion, Susan runs into the male Judas about to attack Chuy, so she distracts it using her blood and causes a train to run into it causing it to be run over and die. Chuy and Susan are then able to escape the tunnel, and shortly afterwards Peter emerges, and the three characters embrace.