Gintoki and his Yorozuya friends (or rather, employees suffering under labor violations), Shinpachi and Kagura, continue to scrape by in the futuristic, alien-infested city of Edo. They take on whatever work they can find while trying not to get involved in anything too dangerous. But when Katsura, the leader of the Joui rebels and Gintoki's long-time acquaintance, disappears after being brutally attacked by an unknown assassin, Shinpachi and Kagura begin an investigation into his whereabouts and the identity of the assailant. Meanwhile, Gintoki takes on a seemingly unrelated job: the blacksmith Tetsuya requests that Gin recover a strange and powerful sword called the Benizakura which was recently stolen. As the two investigations gradually intersect, the Yorozuya crew find themselves in the midst of a major conspiracy that hinges on the sinister nature of the Benizakura sword. Gintoki resolves to take the fight directly to the enemy headquarters, and together with a few unexpected allies, sets out on one of his most perilous jobs yet. [Written by MAL Rewrite]

Hoping for a fresh start, househusband Masaki Fujiyoshi, his spouse Hiromu, and their toddler son, Hikari, move to a new neighborhood. The couple's union was frowned upon by many due to Masaki's status as an omega—a secondary gender that allows an individual to give birth. Even for an alpha—seen as the superior secondary gender—such as Hiromu, discrimination seems to be commonplace and a hindrance to a life of domestic bliss. Fortunately, the new family is not alone. Little Hikari becomes attached to Yuuki Hirai, the Fujiyoshis' lonely college student neighbor. Despite his initial reluctance, Yuuki ends up befriending the infant. Moreover, the family can also confide in Hiromu's childhood friend and coworker Tomohiro "Matsu" Matsuo. Although everything is going well for the young couple and their child, a sudden presence from the past might pose a problem for the peaceful life they dream of.

Three years into the war, Mahito Maki loses his mother in a tragic fire at the hospital. Shortly thereafter, his father marries Natsuko, the younger sister of Mahito's mother. They take Mahito out of Tokyo to seek refuge in his late mother's rural family home. There, Mahito is constantly taunted by a strange gray heron, who seems to have taken an interest in him. Unable to come to terms with his loss and struggling to adjust to a new life in an unfamiliar place, the boy is shocked to discover that Natsuko is pregnant. To make matters worse, the pesky heron can speak—and claims that Mahito's mother is still alive. Luring him into a mysterious tower near the residence, the heron says that Mahito can save her from death, but the boy is not easily swayed. When Natsuko disappears one day, however, Mahito watches her walk into the tower and becomes compelled to venture in to rescue her. He soon finds himself falling into another world below his, where life and death seem to be entwined. As he navigates through this foreign realm to find Natsuko, Mahito must understand what it means to live if he wants to safely return home.

Iroe Genma is a third-year high school student often referred to as "Elder Sister" despite her short height. This troublemaking teenager is the president of her school's Model Club, which is dedicated to building plastic models of various objects and structures, such as cars, boats, and even robots. Joined by her two underclassmen, the violent Hazuki "Okappa" Okamoto and the rational Makina "Makimaki" Sakamaki, the small group aims to carry out their club duties but are often sidetracked by a myriad of distractions. From battles between club members to lessons on how to confess to your crush, these three schoolgirls get caught up in all sorts of wacky, and downright outrageous situations!