DNAlien II is the continuation of the story concerning a secret government program that developed a unique being from experiments with alien DNA and human embryos. The being they produce from the project, known as GENE (Genetic Embryonic Nucleus Enhancement), is part of the ongoing research of captured or crashed UFOs and the recovered bodies. Following Gene’s escape during the World Trade Center attacks in 2001, he is befriended by Butch North, a citizen of Aurora, Texas,.
While the US Government mounts a nationwide search, Butch tries to hide Gene from the intense efforts the government puts into his capture. They use every asset at their disposal, including satellite coverage, phone taps, vehicle trackers, and transmitters secretly placed throughout his home and vehicles. While they try to determine where he has been hidden, Butch and a small group of close friends work together to keep Gene safe. The matter is further complicated when Gene is introduced to a woman named Leslie and they become involved.
As the search expands to include her, Butch must ensure both of them are removed from the rural area just north of Ft Worth, Texas. Throughout the search, Kevin, a very close friend of Butch, becomes the primary protector and is given the responsibility for their lives. When Leslie becomes pregnant, Butch and Kevin are forced to develop plans that will protect them after the baby is born. The government finally learns of Gene and Leslie’s location, and once again they must try to flee the area before they are captured.