Rogue units are members of Civil Protection that, similarly to Barney in Half-Life 2, are not truly loyal to their employers, perhaps committing crimes and using their authority to be a corrupt individual. It is also possible that they are a spy for the Resistance. They might stay as a member of Civil Protection, or may leave the faction and live in an unpopulated area such as the sewers. Reasons for leaving may include being forced to leave because of their identity being compromised, or perhaps if they joined only to get MPF equipment then bailing. (Note: the latter is often looked down upon. Doing this may get you barred from the Civil Protection faction, depending upon the community's rules).
Higher ranks will likely be unable to go rogue. Either they will have undergone surgery to replace their memory and be provided with internal augmentations, they will be addicted to the power they have, or their equipment may be able to track their movements.
Since the nature of rogue units provides a developed character with equipment, the concept is often looked down upon, and many servers will not allow this to happen. Before considering going rogue, you should check the rules of the individual community to see if it is allowed or not.