Enforcer Teppei Sugou, former ace pilot of the National Defence Army's 15th Integrated Task Force, is visited by a scout from the Ministry of Foreign Affairs and invited to rejoin the military. While considering the offer, he recalls his last months of service. His last mission, Operation Foot Stamp, had been a highly classified military strike against the Southeast Asian Union. The operation quickly went south for the ground forces, and Sugou's First Guardian drone was ordered in as air support to drop emergency supplies for the ground units and then return to base. Following orders against his own judgement, Sugou abandoned his comrades on the field. Many lives were lost during the operation, including Itsuki Otomo, Sugou's commanding officer. However, three months later, following a massacre at the Ministry of Defence, Otomo was spotted at the scene on camera. Now a suspect in an act of terrorism, Sugou cooperates with Enforcer Tomomi Masaoka and CID Division One as they hunt his former mentor down.

Shinya Kougami continues to wander the Southeast Asian Union (SEAUn) away from the eyes of the Sibyl System in Japan. While travelling through the Tibet-Himalayan Alliance Kingdom, Kougami encounters Guillermo Garcia—commander of a paramilitary group attempting to unite the local factions and bring peace to the war-torn nation. Wary of joining another mercenary group, Kougami declines to join his cause, but agrees to be driven to the nearby Tibetan capital by one of Garcia’s men. However, Kougami's plan to remain uninvolved is short-lived when a bus of refugees are ambushed by armed guerrillas. Among them is a half-Japanese, half-Tibetan girl named Tenzing Wangchuck. Impressed with Kougami's fighting prowess as he single-handedly takes the attackers out, Wangchuck requests him to teach her how to fight so she can take revenge against the warlord who murdered her family. Knowing first-hand that there's no turning back to the person you were once you take a human life, Kougami is initially reluctant to accept her request. But faced with the girl's desire for vengeance that mirrors the haunting abyss inside his own heart, will he train her?

In Shinjuku ward's east side lies Kabukichou, a vibrant city of chaos that glows brilliantly with neon lights but also hides unseen darkness. Employed at a university hospital on the west side, John H. Watson is looking for someone who can assist him with an odd case. His search leads him to the Pipe Cat, an underground bar that serves as a meetup venue and job board for some of the best detectives in Shinjuku, the most prominent among them being Sherlock Holmes. Upon finding the bar and meeting the peculiar investigators, John learns that they are pursuing a case involving Jack the Ripper, an infamous serial killer. Due to subsequent events, John ends up driving Sherlock to the crime scene of a murder supposedly carried out by Jack the Ripper. Even though John is only there to enlist Sherlock's help with his case, he witnesses Sherlock brilliantly uncover the truth behind the crime scene. However, he begins to realize that Sherlock is not only a genius detective but also an eccentric character. As John continues to request Sherlock to assist him with his case, he finds himself spiraling into the detective lifestyle of solving cases beyond the minds of ordinary civilians. Through this work, John begins to see the true colors of the chaotic city that is Kabukichou and starts to unravel the unsettling mystery behind his own case.

Saya Otonashi is a seemingly ordinary girl living a mundane life with her adoptive family in Okinawa City. In fact, her only peculiarities are suffering from anemia and being unable to remember any of her life beyond the previous year. However, Saya's forgotten past quickly comes back to haunt her—one night, she is attacked at school by a creature that feeds on human blood. Just when all hope seems lost, a mysterious man named Haji appears and fends off the creature temporarily. But when her rescuer forces her to drink his blood, Saya suddenly enters a trance and slays the monster with ease, using her own blood as a catalyst. Saya then learns of an organization named Red Shield, founded for the sole purpose of defeating the hellish beasts. Now Saya and Haji must work together with Red Shield to fight these fearsome monsters and unlock the secrets to the girl's past.