In this continuity, Badniks are not roboticized animals (unlike other continuities, such as the Archie Comics series). Rather, they are autonomous robots that can install animals as "organic batteries" or "power sources". The presence of an organic battery also acts as a defense mechanism: Sonic is forced to hold back the strength of his Spin Attacks for fear of harming the captive within.
Following Robotnik's downfall and establishment of a new base on Flickies' Island, the majority of subsequent Badniks used Flickies as their organic batteries. The Flickies apparently were ideally suited to be organic batteries, and the new Badniks were harder to defeat than Robotnik's previous models.