AtonementShinjiro feels absolutely awful about killing Ken's mother, even though it was an accident. He attempts to escape the pain and admits that he wanted to forget about what happened. However, even during that period of time, Shinjiro constantly punished himself. He left SEES to escape the pain, but leaving SEES also meant cutting himself off from his friends. Shinjiro felt he no longer deserved their companionship, trust and affection. He didn't go to school anymore and thus gave up any chance of meeting anyone else or bettering his future. Additionally, he left the dorm and likely lived on the streets with nowhere else to go. He had barely any possessions when he moved into the dorm the second time and his comment to the protagonist about going back because they had somewhere to go back to implies to me that he didn't have a home during his two years away from SEES.
Perhaps the largest punishment he took upon himself was Persona suppressants. He took them in order to forget about what happened, yes. However, he also accepted them knowing they would slowly kill him as well. He hated himself for what happened both to Ken's mother. Shinjiro believed he deserved to die and was not afraid to do so as punishment for killing someone else. I would not be surprised if killing himself crossed his mind, but I'm sure he felt slowly dying while suffering the side effects of the pills would be more of atonement. When spending time with him at a cafe, the protagonist sees Shinjiro have a coughing fit. He tells her that it happens frequently and not to worry about it. After cooking for a few hours, Shinjiro is completely wiped out and has another coughing episode before excusing himself to his room. While he does not let on to other symptoms, Takaya alludes to him being able to tell he was near death based on what he felt in his body. Therefore, I'm sure he was in constant physical pain as well. His body was probably slowly starting to fail. He always has to wear his coat and knit hat because he can no longer maintain a proper body temperature, for example. Regardless of the exact nature of the suppressant side effects, Shinjiro was clearly suffering. Did he complain about it? No. He did things like avoided cafes in order to not bother the staff with his terrible coughing. Being alone and suffering until he died were things someone like him deserved.
Even after rejoining SEES and gaining a stronger sense of atonement by being near Ken, he still continued to keep everyone at arm's length. Or he tries to, anyway. The protagonist manages to weave her way into his heart, which causes his resolve to waver ever so slightly. Despite enjoying time with her and thinking about her day and night, he still says things like, "haven't you wasted enough time on me?" and "don't bother with someone like me." Without getting too much into their relationship here, his self-hatred becomes fairly evident in their interactions the closer they get. Being with her confuses him because he longs to be with her but feels he shouldn't because he doesn't deserve anything but suffering and death.
Somehow, Shinjiro gets a sense that Ken has plans to kill him on October 4th, the day that his mother was killed. He agrees to meet Ken even when knowing this because he feels it is the only way for him to truly pay for what he did. Shinjiro gives Ken a warning about what will happen to him emotionally if he kills someone but tells him honestly he will not resist if he decides to go through with it. Ultimately, Shinjiro dies (or goes into a coma) by taking two bullets in order to save Ken's life. Even while dying (or thinking he is dying), he doesn't say anything about the pain or having regrets or fears. Rather, he looks at death right in the face and accepts his retribution. He asks Akihiko to continue to take care of Ken for him and seeing the protagonist crying, he manages to say,