Kotetsushin Jeeg takes place fifty years after the original and features a new cast of characters—primarily the new main character Kenji Kusanagi, a high school student who becomes Kotetsushin Jeeg to fight the sudden reappearance of "Haniwa Genjin" ("Haniwa Phantom Gods", or clay robots) from the Jamada Empire ruled by Queen Himika. Other characters include Tsubaki Tamashiro (grandaughter of Miwa Uzuki); and Kyou Misumi. Other main characters from the original series also appear.

This anime adapts Key's visual novel Kud Wafter, which follows the romantic relationship between Riki Naoe and Kudryavka Noumi from the game Little Busters!

Hiroshima, summer of 1945. A young girl named Nobuko saves a starving kitten from crows. She wants to keep the kitten, but her parents dismiss the idea. Nobuko eventually convinces them to let her keep it. She and her brother Makoto name the cat Kuro. Kuro quickly brings joy and laughter to the family. As World War II takes its toll on Japan, it becomes harder for Nobuko and her family to care for Kuro. One August morning, Kuro begins acting strangely...

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.