Ben Day has always been the odd man out. He's the only male in a house full of women. He's one of the only members of his family to survive a mass killing. And, as an adult, he's the only one of his family members in jail. Rough life.
As a teenager, Ben rebels because that's what loners do. In our opinion, as far as rebellions go, this one is pretty minor. Ben listens to death metal and he dyes his hair black. "His hair matches his clothes now" (2.52), Debby says, which shows us that Ben is also a bit goth. Considering how terrible a mother Patty thinks she is, if the worst of her problems is wiping up hair dye from the sink, she's doing pretty well.
However, we quickly learn that the hair dye and the clothes are superficial, just like hair dye and clothes are. They're a cover up for who Ben really is. Being a Day like Libby, though, means that Ben has no idea who he is. So, as teenagers do, Ben copies his identity from his friends. Except Ben has no friends. He only has his girlfriend, Diondra, who is a selfish, angry, terrible person. Therefore, Ben's selfish, angry, terrible side comes out in full force.
According to Patty, Ben has "a taste for hurt" (21.100). Ben vents his anger through physical violence. He screams in the janitor closet and, near the end of the book, lets out all his rage when Diondra and her friend Trey sacrifice a cow. Ben makes it look like a fatality from Mortal Kombat, thinking, "The feel of killing, there might be an empty spot just waiting to be filled" (27.50). Most of this serves as foreshadowing and misdirection, with Gillian Flynn trying to trick us into thinking Ben had the rage to kill his family.
But he didn't. Diondra did. When Michelle catches Diondra mentioning she's pregnant with Ben's baby, Diondra kills her. So Ben is innocent… or is he? Why doesn't he try and stop Diondra at all? Sure, he never liked Michelle, but is that reason enough to want her dead? Perhaps, as a teenager, Ben didn't understand the true consequences of his actions.
Ben makes a lot of actions that he doesn't understand the consequences of. The worst is that he never denies committing the murders, thinking that killing his whole family would make him "admired at school for being such a bad-ass" (8.59). Yeah, because kids love serial killers.
Ben also lets a younger girl kiss him, starting the worst game of telephone ever. As the gossip spreads, the police eventually come to think Ben has actually molested young Krissi Cates. Ben doesn't make matters better when he steals girls' underwear, but he's totally doing that so his daughter will have clothes. Ben also writes "Krissi Day" in a notebook, leading Patty to think Ben is in love with young Krissi, when he really just likes the name for his own daughter.
Ben is simply trying to be the father his own deadbeat dad, Runner, never was. But he doesn't know how, because he never had a good fatherly role model. As a result, Ben has been scrambling for anything he can to make an identity for himself. When he finally gets out of prison, "He felt like he'd been gone his whole life" (41.8).
Out of prison, Ben wants nothing more than a relationship with Libby, his younger sister and the only member of his family left. As we're told early on, "only Libby knew how to disarm Ben" (2.16) when they were kids. She was his favorite. And since he didn't save one of his sisters, he now wants to protect the one remaining. Maybe he would have made a good dad after all. (Probably not.)