Apu is rarely shown in the pieces, as he has been murdered. 

His death is offscreen but clues to the nature of his demise are given throughout, most notably in the Cletus and Glick video which includes the article by Snake which reads.

"Who killed Apu? By Snake (Journalist, Criminal)

Apu was found dead in the Quickly Mart. Teeth removed. Batteries inserted into anus. Eye sockets filled with squishee. Who killed him?

There were no wittnesses no one saw this death. Is this the perfect crime? Who killed him? Apu was a close friend of mine. When I was out of jail I would eat his beef jerky and take my passport photo in the booth. He was warm and friendly. A great guy."

Snake would be the first suspect in Apu's death, as their relationship dynamic was established in the TV simpsons. This does not satisfactorily explain why Snake would write the article.

Due to the violent nature of the crime it is more likely Apu was killed by someone under the influence of Doif.

There is also the fact that the Quickly Mart was taken over by ManMole, and turned into a purse shop, which may have been a motivation as Moe's Tavern and the Quickly Mart are the two main places where characters would get Doif from.