The player plays as Kimura Masaya, a chikan - a pervert - who frequently fondles women in crowded subway trains. One day, a high school girl named Kiryuu Aoi has Masaya arrested for molesting her. Freed after only a day by his influential father, Masaya plans to exact his revenge on the girl. Tailing her, he discovers that she lives with her sister and their widowed mother. Putting plans into motion, his first victim is Manaka, Aoi's younger sister; he rapes her in a public bathroom. His next target is Yuuko, the mother of the two girls, whom he rapes in a secluded park. Aoi is Masaya's final target, the girl who had him turned in to the police. He forces her to go with him to a hotel - owned by his father - after coercing her with photos taken of her mother, then ties her up and rapes her.
After the player completes the initial storyline mode, the player gets to rape them in any situation of his choosing; this is the source of the enhanced replay value in RapeLay (and also the source of the pun in its name). This mode is called Training mode. In this training mode you can "break" each of the three women in nine different ways. Once they are fully broken, the girl will no longer resist your requests during training mode.
Despite being an open-ended game with no real story conclusion, there are two possible negative circumstances which will force the game to end.
The main character impregnates at least one of the girls and decides to keep the child. The result is having the main character thrown onto the train tracks after a certain number of days afterwards. This ending is avoidable even if you do get a girl pregnant - at some point, the game will ask the player whether he wishes the girl to have an abortion.
If the Cowgirl sexual position is ever used with Aoi before she has been Broken, at some point during a subsequent Cowgirl session –even after she is Broken– she will whip out a knife and stab the Masaya repeatedly in the chest. She will continue stabbing while laughing hysterically as the scene fades to black.
The Epilogue reveals Aoi's fate as being held by the police for questioning for the killing.
Even if Aoi is completely naked during the session in which the Ending occurs, she will still be able to produce the knife. As a point of interest, if you observe her from the left side, you can see the knife magically appear.
The above conditions are all it takes to trigger this Ending even if her mother and sister are not subjected to any training sessions at all.