In Persona 3 Portable, Junpei opens up to the new protagonist, letting out a lot of emotions that were built up from his past. He asked the female protagonist if she wants to get something to eat, and she says yes. Before they go into the store, he notices a middle-aged man standing off in the corner staggering around, yelling. Junpei gets angry because the man is clearly drunk and it's the middle of the day. He tells her that he wants to stay away from the man because he doesn't want to "deal" with it. He says, "I mean, if he gets hit by a car or something it's his own damn fault." The drunk looks at Junpei, making him get furious, screaming at him to leave them alone. They run inside the Ramen shop, and Junpei tells her not to talk to guys like that because she could get hurt. He apologizes for acting so weird, but he says that he doesn't like seeing people like that. He brings up the fact that the female protagonist doesn't have any parents, and he apologizes in advance for sounding like an asshole, but he says he "envies" her. He says: "There has to be some parents that their kids would be better off without..." He explains that his dad was always drinking, even when he was all by himself. "Every time he did, he'd get violent over the stupidest stuff..." He told her that he used to act up over it when he was a kid, and his consequences would be that he would get spanked. He notes that it doesn't hurt him at all anymore, however. His father was losing his strength, and it was hard for Junpei to notice it. Junpei stops the conversation early because he realizes he is ranting, and tells her to eat her noodles before they get too soggy.
In Persona 3 FES: The Answer, the Fourth Door leads you to some information on Junpei's past. It zooms in to Junpei sitting alone pondering on how low it must be to get drunk on cooking-wine. He feels badly about himself for running away every day as well, and comments on how he has nowhere to go anymore. His friends walk by and ask him to come with them to a club to drink some booze, saying "you snooze, and you get no booze!" Junpei passes. They tell him to come with them and "live a little!," as Junpei glares at them, saying sternly that he isn't in the mood and will pass. They get nervous and leave. After the flash back ended, he was a bit embarrassed that everyone saw that former memory of Junpei's. He explained that fighting shadows and going to the Dark Hour seemed a lot more appealing to him then going home and dealing with his "old-man."
This constant battle between his home life and his identity is what causes Junpei to get overly angry, depressed, and to feel like he doesn't have anything that special about himself. Junpei lost a valuable relationship - one with his father, which caused him to suffer. Before he had S.E.E.S, he had no one but himself. That is why he decided to change the world, so he could rid it of people like his father. It is very depressing that he had to go through all of that at home, but it was what awoke his Persona from the inside.