ProtagonistShinjiro never became that close with the original male protagonist. However, he can become very close to the female protagonist if the player choses to do so. Though he takes a while to open up to her and discuss things besides fighting and the team, she manages to break down his masquerade and become a precious person in his heart. Slowly, but surely, the player can see how she is becoming increasingly important to Shinjiro as time goes on.
Why could she, of all people, break through Shinjiro's act? Ultimately, I think it was mostly just the timing of their meeting. Shinjiro had been shutting others out for a long time--he was very lonely and bearing pain and guilt on his own. Suddenly, a bright and cheerful girl who wouldn't take no for an answer came along. She enjoyed spending time with him and the more they did, he realized how much he wanted to be with her. Despite all his self-hatred and guilt, he found himself wanting to be with her, too. He wanted to protect her from himself but couldn't say no when she wanted to spend time together. He was unable to stop thinking about her day and night! Even though he had a strong resolve regarding his atonement, he couldn't help but faltering when it came to her. If all he deserved was pain and suffering, why did he feel so at ease and happy when they were together? Why did she love him even though he was a terrible person? Again, he forced himself to be alone for so long that her even wanting to be around him was a blessing he couldn't make himself refuse. I think he fell for her before he realized it, and by that point, it was too late. She was already in his heart. Her smile was enough to make him happy.
Although he never directly discusses his plans for atonement with her, I feel she helps him through the final stages of coming to terms with it. After maxing out his social link, Shinjiro tells her he is okay now because he felt better after their talk. Just by being with him and having someone to talk to made all of the difference in the world. Further, he found someone he truly trusted. That is not to say Shinjiro didn't trust Akihiko, however, it was just a different kind of trust. Shinjiro was clearly worried about leaving Akihiko by himself and it appeared he was completely relieved to know the protagonist would stay by his side. Feeling comfortable leaving everything to her was like a weight lifted off his shoulders. He decided to be Akihiko's support ever since they were kids and thus it was a responsibility he took seriously and prioritized for a long time. Passing the responsibility to care for such an important person to her clearly shows how deep his trust in her is. He certainly would not entrust Akihiko to just anyone.
I also feel the protagonist helps Shinjiro begin to heal. If they had more time together, perhaps she could have helped him through all the pain and grief he had been shouldering on his own. Regardless, her love for him despite his attempts to push her away had a huge impact on him. He begins to show more emotions the more they spend time together. He talks about his feelings with her, albeit indirectly. He embraces her and allows himself to be happy when he is with her. She even gives him the courage to throw a party at the dorm even though something like that would be out of character for him! During the final rooftop scene when she is falling asleep forever, Shinjiro talks about how even though he forgot everything else, his feelings for her never changed. She was always precious to him. For Shinjiro to be that open about his feelings about someone else required him to open his heart--something he had not done in two years. She truly left a lasting imprint on his life.