McKenzie Files.

The United Protectorate is under attack by the Brelac, a bloodthirsty reptilian alien race bent on destroying humanity. A dark alliance between the Brelac and the Vendetta, a separatist organization, looms over the Protectorate. The Brelac's onslaught brings forth the creation of the genetically engineered humanoid weapons called Reploids. Reploids are identical copies of real humans captured, killed, cloned, embedded with powerful psionic abilities, and programmed to serve the Brelac. They are untraceable and blend into human society so believable, that even the Reploids themselves do not know they are clones. Lead character Colin McKenzie, part of a military team sent to a remote planet to investigate and capture a downed Brelac ship, turns on his commanding officer in an attempt to protect a shipwrecked band of Brelac soldiers. But he is captured and reprogrammed, along with two other captured Reploids to serve the government they were originally created to destroy. The balance is upset when a weapon powerful enough to bring the Protectorate to its knees is about to be unleashed. And the Protectorate's only hope of stopping it are the three Reploids.