Benji is around for quite some time in the book. He's as douchey as they come and a wealthy former drug addict who cofounded an organic club soda company called "Home Soda." It's clear he's just using Beck for sex, but it's also clear that she has genuine feelings for him that aren't going away anytime soon. That spells out a pretty big problem for Joe, who now can read all Beck's emails back and forth to her friends because he has her phone (she doesn't tell her mom it went missing because she doesn't want to get in trouble, so the cell remains active).
As he continues to stalk Beck's every move — standing outside her apartment, following her and her friends to the bar — he gradually formulates a plan to take Benji out. He lures Benji to the bookstore under the guise that he's a Vulture food critic interested in reviewing Home Soda and doses a drink he gives Benji with a drug that knocks him out. When Benji wakes up, Joe has dragged him into the bookstore's completely soundproofed basement, where a large "cage" is set up — it's essentially a small, clear room within the basement where first-edition books are kept, outfitted with a bathroom and AC.
Joe keeps Benji there for weeks, putting him through a series of tests: he sees if Benji can identify his own club soda brand, tests him on knowledge of popular books, etc. Meanwhile, Joe breaks up with Beck by texting from Benji's phone (she's furious) and then begins sending tweets from Benji's account that make it seem like he's out of town on a bender somewhere. When it becomes clear that Beck is never going to truly give up her feelings for Benji, no matter how angry she is, Joe kills him by slipping nuts into his latte, which Benji is allergic to.
Image Source: Lifetime