Over three hundred years have passed since the Calamity War, the great conflict between Earth and its outer space colonies. Now Earth is ruled over by four economic blocs, and the military organization Gjallarhorn is responsible for keeping the peace. Mars, on the other hand, depends heavily on Earth's economy. Horrified by the appalling living conditions that Mars' inhabitants have to bear, Kudelia Aina Bernstein, a young aristocrat from the Chryse Autonomous Region, gets involved in the Red Planet's independence movement. She hires the services of a local company, Chryse Guard Security (CGS), to escort her on the journey to Earth to negotiate economic conditions with the earthly bloc that controls the region. The Third Army Division—consisting of Mikazuki Augus, Orga Itsuka, and many other child soldiers—are chosen to protect her. When Gjallarhorn attacks the CGS facilities to assassinate the young revolutionary threatening their interests, Orga and his comrades must not let the attackers accomplish their goal—in fact, Gjallarhorn's actions might turn out to be the unintentional catalyst that leads the children to be the forgers of their own destiny. [Written by MAL Rewrite]

At the end of season 2. Yuuri defeats Shinou, but since Shinou had been defeated, Yuuri and Murata could no longer go to the Shin Makoku. However, because Yuuri had fought and defeated him, his powers had surpassed that of Shinou's, resulting in him being able to rely on his own power to return to Shin Makoku. After the ceremony at the age of 16, Yuuri slowly begins to discover that much has happened while he was away. The ten officials of the noble family have decided to make Wolfram the next Maou, but now that Yuuri has returned and taken back his role as Maou, complications arise when one noble disagrees with Yuuri returning to the throne. In addition, an ancient secret society that threatens the peace of both humans and Mazoku has risen, and a fight for the throne that now leaves the nobles wondering who is the legitimate Maou.

One could say that freshman college student Tadayasu Sawaki has a wide range of vision. He has a peculiar ability that allows him to see microorganisms with the naked eye. Sawaki can see all sorts of microbes, from the fungi that cause athlete's foot to the yeast used to make alcohol, with him perceiving his little friends as cute chibi creatures. Attending an agricultural university, his talent piques the interest of numerous professors, including Professor Itsuki, who specializes in fermentation. Sawaki starts school indifferent toward his ability, choosing an agricultural school in Tokyo. However, with the help of the eccentric community around him, he slowly learns to appreciate these visible microbes and his talent. The whimsical cast of professors and classmates attending the university almost makes Sawaki seem normal despite his ability. [Written by MAL Rewrite]

A new special episode that was distributed to those who purchase all three Blu-ray box sets of Sayonara Zetsubou Sensei series on January 31, 2012.