Sin and Punishment is set in a dystopian near future of 2007, when humanity is struggling with a planet-wide famine. To solve this problem, scientists develop a genetically-engineered species to raise as food. These creatures are herded in
northern Japan until they mutate and begin attacking the country's citizens. They are dubbed "Ruffians". An international peacekeeping organization called the Armed Volunteers tries to stop the creatures, but they also oppress the Japanese people. Another group, led by a mysterious woman with unusual powers named Achi, rises up to defend Japan against the Ruffians and Armed Volunteers. Within her group are Saki and Airan, the male and female protagonists of the game. Between battles with the Ruffians and Armed Volunteers, Saki unintentionally morphs into an enormous Ruffian after falling into a rising tide of blood filling up
Tokyo. To bring Saki back to normal, Achi tells Airan that she will need to shoot Saki, but Airan refuses to do this. In response, Achi places Airan into a dream sequence, set ten years in the future in
Long Island, New York. Here she meets her future son she shares with Saki, and sees a Ruffian Saki rampaging through the city. The dream ends with her shooting Saki, and waking up to realize that Achi manipulated her through the dream into having just shot the real world Saki in the present. After Saki fights Ruffian forces in
Hokkaido and Airan is kidnapped, Achi reveals that she is not from Earth, and that the war between the Ruffians and the Armed Volunteers was her ploy to groom Saki into an ultimate warrior to use in a cosmic battle with extraterrestrial beings. She reveals that Saki would help her rule the new Earth she is about to create. Achi creates a new Earth and begins attacking the current Earth. Saki, in a part-human, part-Ruffian state, combines with Airan to revert to his full-Ruffian form while maintaining self-control. Saki and Airan successfully destroy the new Earth and send Achi drifting into space. After the battle, Saki and Airan revert to their human forms and descend back into Japan, which the battle with Achi has left in ruins. Airan questions what she and Saki will now do, after which they decide to take on the rest of the Ruffians together. They change back into Saki's Ruffian form and head towards Honshu. Meanwhile, as Achi drifts in space, she notes that with Brad and Saki lost as potential warriors, she cannot hope to win against her enemies, but mentions Saki and Airan's future son Isa, who will inherit the former's blood. Seemingly viewing Isa as another candidate, she says that the time for the enemy to call themselves gods is "coming to an end." ==Development==