Nuclear weapons are old news. They're volatile, wasteful, and completely diminish property values. Enter Project: USA, an initiative to create humans with abilities far greater than normal. These subjects were treated like any other weapon, cataloged, traded, sold, and stockpiled, their every move tracked, any personal connections strictly forbidden. Some of these Ultra Sapiens began to breed with one another, and even the general population. A group of them decided that being under any governments thumb was no longer in their best interests. Led by Steve and Sue Baker, they raided Project: USA and destroyed every piece of data pertaining to the locations, names, and abilities of the Ultra Sapien race. The only copy of this catalog was hidden in their young son's genetic structure to prevent it falling into the wrong hands.
Fast forward 17 years. Project: USA is now the Hunter Killer division, led by the same man who created the process for making Ultra Sapiens possible. He is known as Morningstar. His team consists of Ultra Sapiens that for various reasons track and hunt down their own kind. Morningstar has been looking for the catalog since it was lost, and he has located the Bakers and sent in a team for retrieval and elimination.
Ellis Baker knows nothing of his heritage or abilities, having been raised in isolation by his parents. Every Saturday he undergoes intense combat and survival training, but is made to forget that it happens. To him there are 6 days in a week, Saturday doesn't exist. The Hunter Killer team attacks the Baker cabin, Sue tries to hide Ellis in an escape tunnel while Steve engages their attackers. Sue locks Ellis in the tunnel and goes out to defend her family. Her bio-nuclear energy destroys their home and wounds some of their attackers. Wolf, a rogue Ultra Sapien, tries to get the catalog, not knowing it is Ellis. When Wolf grabs Ellis, his powers ignite and copy Wolf's cloaking ability. He escapes the rubble of his home to see his father transformed and fighting the Hunter Killers. Upon seeing that Ellis has not fled, Steve tries to kill his son to prevent the catalog from falling into Morningstar's hands. Ellis copies his mother's powers and regretfully defends himself with lethal force against his father.
The Hunter-Killers are a secret, government-funded organization created to track down all Ultra Sapiens that escaped from Project: USA. Ultra Sapiens that willingly turn themselves in or don't resist when caught are given jobs as part of the team while the dangerous ones are killed.
During the events of the CyberForce/Hunter Killer crossover, Ellis returns after two years of wandering and learning about the Earth and it's people. Uncovering a plot by Morningstar and his new partners, Cyberdata, he arrives too late to prevent a skirmish between the Hunter Killer team and CyberForce. Morningstar fed the HK team false information that CyberForce was really a rogue group of Ultra Sapiens. After breaking up the fight and having Architect save Heatwave's life, the teams agree to work together to stop Morningstar. They split into 3 teams, with the purpose of hitting 3 targets simultaneously.
The heroes are outmaneuvered by their opponents and there serious injuries to Architect and Cloak and several members are captured. Confronting Morningstar, the remaining heroes are able to free their comrades and stop Cyberdata from unleashing a viral signal that would effectively turn a large portion of the general population into Ultra Sapiens, who would have no idea how to control their newfound powers. They accomplished this by killing one of their own, Network, and installing Damper into the system that broadcasts the U-S virus. CyberForce member Velocity is infected w/ the virus, and after the conflict, Ellis joins CyberForce to help keep her new situation in check. Heatwave joins the HK team to keep an eye on them.