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Maya (Bianca Lawson) was tragically murdered in Season 2, Episode 25: “UnmAsked,” but at least the mystery of her death didn't take as long to solve as that of poor Alison's (Sasha Pieterse). In the Season 3 summer finale Maya's killer was finally revealed, and it was …
Everyone who thought that Nate was not Maya's cousin but actually her stalker ex was totally right. "Nate" was actually Lyndon James (which answers the "who is LJ?" question). He was obsessed with Maya, and it seems that he killed her after she spurned him.
Meanwhile, in this episode he decides to go after Emily (Shay Mitchell) by killing Paige (Lindsey Shaw). Fortunately, Emily gets away and distracts him from Paige, and after a struggle she ends up killing him to save her own life. In a way, she did avenge Maya, too.
Though, worth noting: Nate never said the words "I killed Maya." Is it possible we don't have the full story?
UPDATE: PLL writer Bryan Holdman confirms Nate is Maya's killer.