After a strategic maneuver, Senkuu Ishigami's team stalls Dr. Xeno's more scientifically advanced forces. A ceasefire between the two factions allows for the establishment of Corn City in North America, a hope for a future thriving population. Meanwhile, Senkuu and some of his teammates rush toward the Amazon in South America—the epicenter of the petrification beam's impact—to create Superalloy City and progress their spaceship project. With dangerous enemies still pursuing Senkuu and his companions, it is a race against time to reach the heart of the dense Amazon. As unexpected allies and scientific creations further fuel this leg of their journey, Senkuu is closer than ever to finally uncovering the mystery behind the petrification phenomenon.

Seven years after humanity was devastated by a major disaster, a beacon of science and prosperity rises in Kamitsubaki City. But lurking in its shadows are Tesseractor, monsters born from human darkness. Only the Witchling, five girls with voices that wield magic, stand against them. With every note, they fight, not just to protect the peace of the city, but to heal a broken world.

Following the massive operation that led to the confinement of recent recruit Kafka Hibino, otherwise known as Kaijuu No. 8, the Defense Force has been puzzled by how to deal with him. Kafka is the first kaijuu to side with humans, and after careful consideration, he is eventually transferred to the Defense Force's First Division in the hope of adding his power to the strongest division, capable of handling any threat. However, some people are still doubtful about Kafka, and he must prove his worth in the next mission. Kafka and the First Division are soon dispatched when a massive horde of ant-like kaijuu begins wreaking havoc. Thanks to the combined strength of Kafka's friend Kikoru Shinomiya and their captain, Gen Narumi, the mission seems to progress as it should. However, when Kafka fails to transform into his kaijuu form, the dreadful Kaijuu No. 9 joins the battle with only one goal—to eliminate him and steal his power. Although the situation is looking grim, Kafka must overcome his most difficult trial yet with the others if he wants to keep pursuing his dream: fighting side by side with his childhood friend and Third Division captain, Mina Ashiro.

On the planet after the disaster, the young boy Ye Yu went to Embers City for an assessment in pursuit of his dream. He faces numerous murderous intentions and mysteries, and the truth behind them is impossible to unravel.