Applewhite had recently been devastated by the death of his father, Nettles' marriage was failing, and generally it wasn't as healthy of a basis for a friendship as, say, a shared interest in Mario Kart.
Entire books have been written about what happened next, but the short version is that, after a period of intense religious studies, Applewhite and Nettles concluded that they were the "two witnesses" referred to in the Book Of Revelations (a popular claim for fringe religious groups), and that they had been given "higher-level minds" to fulfill Biblical prophecies. So they hit the road and started preaching, covering 8000 miles in a single month and going broke in the process. These weren't scam artists demanding payment for salvation -- they were true believers.
Their precise beliefs kept shifting like a philosophy undergrad's, but the gist of what they finally landed on is that the Biblical God is actually an incredibly advanced alien, that the Earth is due to be "recycled" and that, under the right guidance, humans can ascend to "The Evolutionary Level Above Human," essentially a snazzy sci-fi version of heaven.