Update: When the reality was recreated by Cheryl and Wind, some of the dead Mavericks returned to live. They gave the Special Unit and the Hunters great trouble, but the last Maverick was defeated in Eruasia with the defeat of X and Sigma as the place was destroyed. Currently, the only known 'Maverick' left is the Wiendigo Virus, in the form of the reploid Wiendigo. And the captured Vile, sealed away somewhere.
Old Entry: The Mavericks are reploids who have either been infected with the Maverick Virus and gone insane with hate towards humans, or they're reploids who have simply decided humans are inferior and that reploids should rule over them instead. Either with the humans alive or as corpses. Originally, the mavericks were led by Sigma during the first Maverick War, but they were defeated again and again three times; the fourth war, with Repliforce, ended once again in Sigma's defeat. However, in the process, Zero went Maverick and destroyed a huge portion of Siberia, turning it to a wasteland. Reploids were repressed there, all considered Mavericks.
During the Year Long War in The Alien Wars, the Mavericks were led briefly by Sigma, but he was destroyed. After Vile was destroyed, the leaders passed on to Crucifixtion until they were all defeated along with the Tsivrixsh masters that controlled them. More Mavericks rose up again in The Alien Wars 2: The Galactic Conflict but were wiped out by the Special Unit. Since then, there were no more conflicts until reploid prejudice began to rise, so Death Star went 'Maverick' and had others join his cause, drawing the world into another war. He did so to give everyone an enemy to hate and unite reploids and humans against the Mavericks, while knowing Slasher would prove that reploids had souls. His death paid off and reploids were no longer mistreated.