What happened was that when the cloud dispersed due to the widespread radiation it left the surviving hostile nanite clouds "alive" and unmolested. If these clouds could avoid radiation zones after achieving their programmed missions they could go dormant or find themselves free and with no mission to achieve. Radiation also sometimes caused malfunctions in their original programming leading to unforseen actions and results. Some nanoclouds, prevented from achieving their objectives by these rad zones They too quickly learned the trick of linking with a human and communicating with them to accomplish things they could not.
Over the years these nano clouds have spread and acquired many followers. The smartest have learned much of human psychology and are quite adept at convincing others to follow them. Some of them have developed personalities as well, making them seem even more like angry gods. All of them though tend to be agents of disruption and destruction and violence. It's important that they are not human and they do not care about preserving humanity. Many of them are not especially concerned with preserving themselves. Some have been developed flaws over the years and their goals tend to shift around with no apparent pattern. A few have become concerned with acquiring power and followers and these will even fight other chaotic "gods".