Numerous hours and objections from PETA later, Ajay and the rebels overthrow Pagan Min. He reveals that he wanted to pass leadership of Kyrat to Ajay because his original successor, Lakshmana, was murdered. It turns out that Ajay's father sent his mother into Pagan's inner circle as a spy, but she had a fetish for weedy guys in fabulous suits and Prince was nowhere to be found. When Ajay's father found out, he killed their love child Lakshmana out of jealousy, and Ajay's mother killed him in return before fleeing to America.
You can discover all of this after countless brutal deaths, or you can avoid all the bloodshed and learn everything within the first 15 minutes. If you forego your daring escape and dutifully wait in Pagan's dining room like he asked you to, he'll eventually come back and take you to Lakshmana's tomb while explaining the entire plot. You leave your mom's ashes before going with Pagan to shoot shit up in a highly dysfunctional father/son relationship. It's implied that the despotic leader will groom you to be a "lesser-of-two-evils" ruler, and all you had to do was let the game play itself.
And the music that plays during the intro? The Clash's "Should I Stay or Should I Go?" gives you a little hint that you should probably stick around.