Rather than telling it in the order of the novel, I’m telling the story in a way that’s easier to grasp.
Naoki and Ryou knew each other since they were children as they both lived in the same town close to a mountain. One day when Naoki and Ryou’s two sisters went out to play, an accident happened. Owing to this accident, Naoki felt very guilty and his attitude toward Ryou’s family altered because of the guilt. One day in high school, Ryou suddenly confessed to Naoki! Since he felt guilty inside and did not want to hurt Ryou, Naoki agreed. Ryou was very nice to Naoki and when they both moved to Tokyo to study at a university, they lived in the same apartment. Day by day, Naoki began to fall in love with the gentle Ryou. However, the more he loved Ryou, the stronger the guilt within him became until one day, he could not endure it anymore. So, he escaped by vanishing before Ryou. He dropped out of university, moved from town to town, and was too scared to find a permanent job in case Ryou might find him. Eventually, he worked as a part-timer at a flower shop. The actual story began with their reunion four years later after Naoki’s disappearance. Naoki was delivering flowers to a hotel when he met Ryou. This time, Ryou would not let him run away again. Ryou was very careful as he thought last time Naoki ran away, it was because he hated him. So no matter how much he wanted to have sex with Naoki, he surpressed his own desires and just stayed kind to Naoki (taking him out to dinner because Naoki was thin and did not seem to be eating properly). He also confessed to Naoki once again and said that it did not matter whatever the reason Naoki left last time. As long as he would not disappear before him again, that would be enough for him. Naoki also loved Ryou very much, but his guilt was a major barrier. There’s also Ryou’s sister – Yuri – who opposed to their relationship (after all both of them were men and also because Yuri knew about Naoki’s "secret". Naoki thought that was the reason why Yuri would not let him date her brother. Naoki promised he would not run away again but when he heard news on television that the mountain in their hometown would be flattened to build a golf course, he freaked out. He was afraid his secret would be discovered and then Ryou would really hate him forever. At that point, being hated by Ryou was the worst thing that could happen in the whole world. So, he broke his promise once again and rushed back home.
Ryou of course tried to pursue Naoki and when he caught Naoki at their hometown, he could not control his anger anymore. Mad with rage, he punished Naoki by imprisoning him at the local hotel and had really intense sex with him (4 times) . Despite that, from the insert artwork, you could see how deeply Ryou loved Naoki (and Naoki loved Ryou too). In the end, Naoki could not take it anymore and when they arrived at the mountain, Naoki told Ryou that it was because of him Ryou’s sister died. When they were children, they were playing at the river but Ryou’s sister fell into the river and died. However, she did not really die because of drowning. She had a weak heart and she should not go out to play. She fell into the river because she had a sudden attack and she died of heart failure but of course as kids, they did not know that. Naoki and Yuri panicked. So they buried her body in the mountain. Ryou then told Naoki that he knew all of these (and all along too) . Yuri told the family and they actually dug out her body and gave her a proper funeral ages ago. Naoki did not know that because on the day of the funeral, he was down with fever. Naoki also misunderstood Yuri’s hatred toward him. She actually loved Naoki, but she thought he forgot about her dead sister and so when she saw him with the brother she respected, she was very angry and wanted to break them up. That’s why she kept trying to destroy their relationship. When the truth was all out, Naoki and Ryou reconciled fully and with Yuri on her way to a happy future with a man she loved, Naoki and Ryou could alas smile at each other without fear, guilt, or sadness.