Zon-Kuthon is a twisted, cruel, jealous god who defiles flesh to bring pain and misery. Unrepentantly evil, he finds brief joy in the pain he causes others. His very existence is a corruption and parasite upon the world. His alien mind constantly seeks new ways to oppress, humiliate, demoralize, and destroy others. He whips the minds of serial killers, guides the hands of torturers, and plays the nerves of the suffering like a master bard. He has recently has found that he gets more joy in torturing one's heart and mind rather than flesh, and as such has recently found joy in forcing those who would revile him, to serve him.
Eventually no one was left alive to worship the gods, so they lost all their power and 'died' off. The demigods having a slightly different nature to true gods were able to gain the power left in this power-vacuum to semi-resurrect. With the introduction of the Kadeshi the demigods were able to regain worship and thus some of their power.
With no worshipers, and lacking the cunning of Baphomet to get them Zon-Kuthon leapt at the chance to regain power when Baphomet offered him the chance. Baphomet's plan was to his liking anyway, and gave him opportunity to inject his own fetishes into the various plans. He possessed Solzhenitsyn and made sure that in every project he had a hand in there would be pain and suffering. For example Dark Trooper production and even the research to create them could have been much more humane but with Zon-Kuthon at the helm he was sure that was not the case. Zon-Kuthon was also instrumental in convincing Sarenrae to help Baphomet, as forcing people to help him who would otherwise fight against him is one of his favorite things to do, and something he has centuries of practice doing.