After the Genesis Wave had passed, Eggman found himself alone and imprisoned.
To be blunt, he found his new circumstances quite horrifying. A side effect of the wave was that his senses were impaired to the point of near total deprivation. He was effectively blind, deaf, and had only the barest sensory feedback to tell him that he was even alive. In fact, it took several hours of intense focus on that sliver of sensation to reassure himself that he was, in fact, still alive and he was able to calm down, reflect, and analyze his condition. The good news, he ultimately concluded was that he was quite sure his condition was only temporary. The bad news was that recovery would take time, and that there was nothing he could do to speed up the process. Additionally, there was the strange feeling that he had not been alone during his hours of panic, but who might have visited him he had no idea. Still, in the larger picture it didn't matter. He had his thoughts for company and that was enough