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. This deeply moves Susan and causes her to choose to make a cockroach killing bug called the Judas Breed. When engineering the organism, she ensures that they could not reproduce within the lab. This leads to the belief that the Judases will go extinct after one lifespan. The epidemic is then eradicated after she releases the Judases into the wild, and she and Peter fall in love which leads to them getting 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. Furthermore, 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, along with 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. Thus killing the male Judas would lead to the species extinction. 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, Peter 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, which is about to attack Chuy, so she distracts it using her blood. The Judas begins charging her, however at that exact moment a train comes by, which runs over the bug and causes it to die. Chuy and Susan are then able to escape the tunnel, and shortly afterwards Peter emerges, and the three characters embrace.