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.

The Daichis are a family in danger of tearing itself apart. Dissatisfied and money obsessed mom Seiko has served wimpy and otaku dad Mamoru with divorce papers. Daughter Nozomi who has always been saddled with all the housework, feels pained that everyone is using her. The youngest albeit most foul mouthed, Dai is forced to watch all this as everything is going to pieces. However when the Galaxy Federation recruits the Daichis to combat alien threats to the wellbeing of the Earth, it will be a chance for the family to save the world and maybe themselves.

The One Year War comes to a close, as the Zeon forces now retreat back into space. Amuro learns much more of his Newtype abilities and tries to use them the best way he can. He's pushed to his limit as he encounters the infamous Char Aznable once again. He also falls in love with a mysterious woman named Lalah Sune, who knows the full potential of the Newtype abilities. The greatest battle is about to begin, as many loved ones fall to the power of war. Can the Earth Federation defeat the Principality of Zeon? Or will they fail? Can Char prove that he's the better Newtype than Amuro? They all will be answered now...

In the distant future, humanity is hurtling down a path of ruin. Global environmental destruction caused by chemical contamination, radioactive fallout, and UV rays coming through the patchy ozone layer has lead to deterioration of the human genome.