“Baphomet was the worst of us. Many people in this world have evil in their heart, but Baphomet was chief among them. In his mad search for power he twisted himself into that form, becoming the first Minotaur long before we bound Quetzalcoatl. He wanted to kill just to kill. When victory was in hand he would betray those who trusted him, with no real desire for either side to win, he just wanted to watch the chaos that would ensue. His only allegiance was to chaos, the only thing that would make him smile was pointless destruction. If anyone was fit to take the burden of being the God of Chaos and Destruction it was Baphomet.” - Coriakin
Though defeated the White Witch's many plans to conquer the planet continued after her death. 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.
Baphomet seizing this opportunity appeared very early in Kadesh's timeline and made a bargain with some of them. While it started as a few elves in time their number grew and so did the power Baphomet gained from their worship. When he had enough strength he enlisted Zon-Kuthon and Sarenrae to help him (see Zon-Kuthon and Sarenrae for more info). Baphomet eventually took possession of Kyle Katan and with that powerful influence was able to make preparations to leave this dead world and return to the marooned elves' homeworld.
“I will soon return to the Homeworld and claim it. Follow me and you will ascend, reborn into my likeness. You will join me in the great calamity from the sky, and I will give you the land as your birthright!” - Baphomet's Deal
Worship looks different for every god, for Baphomet among many different rituals and rites taking part in destruction and chaos is what fed Baphomet's strength. He played off of the people's poor circumstances. People were taken advantage of, thrown into a society that was stagnant except for it's oppression of the poor to the benefit of those already wealthy, and Baphomet knew just how to pray on people like that. He fed into their desires for revenge and for action against their oppressors. He knew that in a society that has destroyed all adventure, the only adventure left is to destroy that society, and that is the purpose he gave his people. They were led to destroy everyone, from those in charge to those walking by, to kill all even often themselves in the process. In return he promised their sacrifices and offerings would grant them favor in his eyes and he would transform them into his own likeness, that of minotaurs, and promised them a seat in the afterlife with him that he called the great calamity in the sky.
He never had any intention on keeping that promise.