The story follows the life of Yuu Haruna, who recently moved into Tokyo with his sisters after their father is forced to transfer overseas on work. On his way to buy dinner while looking at his Twitter account, a high school girl suddenly crashes into him. Thinking he was taking upskirt pictures of her, the girl takes Yuu's phone, breaks it, and slaps him before leaving Yuu lying on the ground. As it turns out, this girl—Fuuka Akitsuki—also goes to the school Yuu is transferring to. Unlike most people, Fuuka doesn't own a cellphone; she even listens to music using a CD player. Eventually these two become closer, and decide to form a band with their friends and enter the professional world of music. With Fuuka around, what will now become of Yuu's new life in Tokyo?

Several months have passed since the infamous Ginza Incident, with tensions between the Empire and JSDF escalating in the vast and mysterious Special Region over peace negotiations. The greed and curiosity of the global powers have also begun to grow, as reports about the technological limitations of the magical realm's archaic civilizations come to light. Meanwhile, Lieutenant Youji Itami and his merry band of female admirers struggle to navigate the complex political intrigue that plagues the Empire's court. Despite her best efforts, Princess Piña Co Lada faces difficulties attempting to convince her father that the JSDF has no intention of conquering their kingdom. Pressured from both sides of the Gate, Itami must consider even more drastic measures to fulfill his mission.

Off-duty Japan Self-Defense Forces (JSDF) officer and otaku Youji Itami is on his way to attend a doujin convention in Ginza, Tokyo when a mysterious portal in the shape of a large gate suddenly appears. From this gate, supernatural creatures and warriors clad in medieval armor emerge, charging through the city, killing and destroying everything in their path. With swift actions, Youji saves as many lives as he can while the rest of the JSDF direct their efforts toward stopping the invasion. Three months after the attack, Youji has been tasked with leading a special recon team, as part of a JSDF task force, that will be sent to the world beyond the gate—now being referred to as the Special Region. They must travel into this unknown world in order to learn more about what they are dealing with and attempt to befriend the locals in hopes of creating peaceful ties with the ruling empire. But if they fail, they face the consequence of participating in a devastating war that will engulf both sides of the gate.

When Gintoki apprehends a movie pirate at a premiere, he checks the camera's footage and finds himself transported to a bleak, post-apocalyptic version of Edo, where a mysterious epidemic called the White Plague has ravished the world's population. It turns out that the movie pirate wasn't a pirate after all—it was an android time machine, and Gintoki has been hurtled five years into the future! Shinpachi and Kagura, his Yorozuya cohorts, have had a falling out and are now battle-hardened solo vigilantes and he himself has been missing for years, disappearing without a trace after scribbling a strange message in his journal. Setting out in the disguise given to him by the android time machine, Gintoki haphazardly reunites the Yorozuya team to investigate the White Plague, and soon discovers that the key to saving the future lies in the darkness of his own past. Determined to confront a powerful foe, he makes an important discovery—with a ragtag band of friends and allies at his side, he doesn't have to fight alone.