At Daimon High School, kids settle their disputes by dueling with each other in the school's official K-Fight battle arena. Ryoko Mitsurugi, samurai girl and undefeated K-Fight champion, is called upon by a mysterious Priestess to protect the Earth from an invasion coming from the alternate universe of Solvania. She must face battles that will test her skills, her friendships, and her heart in order to find her true strength as a samurai warrior. (Source: ANN)

A member of the Time Patrol finds out that there is a disturbance in Japan, 1570. While heading to that particular time and location to investigate, she is attacked and ends up stuck underground the Nohara residence at the end of the 20th century Japan. Having limited resources at hand, she is forced to ask for the help of the Nohara family. Together they go back in time and meet with a samurai named Fubuki-maru who believes that they are the legendary three persons and dog whom someone from her family would eventually meet in a crucial moment. The lonely samurai asks for their assistance in defeating the man that possesses strange magical powers, the sinister Unkokusai lord. (Source: ANN)

In 2029, a large scale ground sinkage occurred in the Mediterranean Sea. Chemical elements such as oxygen, carbon, gold, molybdenum, and cobalt disappeared from the earth's crust suddenly. The human population was decreased by 90% in sixty years. Researchers found out that the disappeared elements were drained into a planet "Nega Earth", located in another dimension. To save the Earth, a special team called the "Element Hunters" is organized. All of the members are under 13 years old, because young and flexible brains are needed to access "Nega Earth".

Continuing where the first season left off, the sudden increase of Thanatos with the disappearance of the Aube Hunters has now left Arcadia in ruin. Desperation reigns high as the Religious Organization fights to battle the Thanatos. Six months had already past since Hidamari mansion burned to ashes, the Aube Hunters, once hailed as heroes, is now blamed for the appearance of Thanatos. Nevertheless, hope still exists for the reappearance of the Queen's Egg one day, who will become the savior of Arcadia. Unknown to many however, the Aube Hunters have actually been silently waiting for the awakening of Angelique, who has been asleep the entire time.