Half a year has passed. Arriving in the Iron Fortress, Ikoma and Mumei set foot in Unato: another ravaged zone that fell into the grip of the deadly Kabane. In this war-torn zone, the group fends off more dangerous Kabane that are attacking with patterns they had never seen before. The Iron Fortress crew eventually meet up with a survival group which requests their aid in reclaiming the zone. The newly forged alliance ventures deeper into the area of the castle and investigates the peculiar case of these new Kabane. But their search for answers unearths truths that are far more horrifying than they imagined. Forced to confront the reality behind the Kabane, Ikoma, Mumei, and their allies come to realize the despair buried within Unato.

The world is in the midst of the industrial revolution when horrific creatures emerge from a mysterious virus, ripping through the flesh of humans to sate their never-ending appetite. The only way to kill these beings, known as Kabane, is by destroying their steel-coated hearts. However, if bitten by one of these monsters, the victim is doomed to a fate worse than death, as the fallen rise once more to join the ranks of their fellow undead. Only the most fortified of civilizations have survived this turmoil, as is the case with the island of Hinomoto, where mankind has created a massive wall to protect themselves from the endless hordes of Kabane. The only way into these giant fortresses is via heavily-armored trains, which are serviced and built by young men such as Ikoma. Having created a deadly weapon that he believes will easily pierce through the hearts of Kabane, Ikoma eagerly awaits the day when he will be able to fight using his new invention. Little does he know, however, that his chance will come much sooner than he expected...

In 2039, helper androids are widespread as general purpose electronics. Keiichiro lost his family in a traffic accident and retired from his band. One day, he finds an android of an old model in a garbage dump. He takes her home, but after taking her to a repair shop he was told that she couldn't be repaired, so he plans to throw her away. The next day, Keiichiro finds her making breakfast for him. Thus begin the summer days of an android with no memories and a dreamless boy.

Following an accident where Masato Inohara batted a baseball into the school's water main, the boys' dormitory is partially crippled. Until a plumber repairs the damage, the boys have to stay in the girls' dormitory. To determine which rooms they'll be assigned to, they draw tickets from a hat. Unfortunately, due to the limited capacity, some of the boys will have to go without a bed. Once Riki Naoe draws his ticket, he gets one that forces him to stay in one of the less-than-cozy clubrooms. Seeing his hapless predicament, a nervous Kudryavka Kud Noumi musters enough courage to confront her feelings while asking Riki to sleep in her room instead. Despite the rest of the Little Busters incessantly teasing Kud and Riki about their relationship, he stays with her throughout the summer. As they share unforgettable experiences one after another, the two realize that they might want to be more than just friends.