In Universal Century 0079, forces of the Earth Federation and Principality of Zeon engage in a battle within the Thunderbolt Sector during the One Year War. This section of space—known for its constant strikes of electricity—proves to be a deadly battlefield, as Federation pilot Io Fleming leads a charge against Zeon's ace Daryl Lorenz and his squad of snipers. With the fighters on both sides proving to be formidable soldiers, neither side is willing to back down, fighting strategically amongst the remnants of colonies. But when Io gets a hold of a prototype Gundam, Daryl will have to make a sacrifice in order to obtain enough power to crush his enemy and ensure that Zeon is victorious, or watch as his comrades are slaughtered by a single man.

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.

Manji is an infamous swordsman in feudal Japan who is known as the Hundred Man Killer, as he has killed one hundred innocent men. However, there is something far more frightening than his ominous reputation: the fact that he is immortal. This is the handiwork of eight-hundred-year-old nun Yaobikuni, who placed bloodworms capable of healing almost any wound in Manji's body. To atone for his crimes, Manji resolves to kill one thousand evil men. Yaobikuni agrees to this proposal, saying that if he succeeds, she will undo his curse of immortality. Soon after this promise, Manji meets Rin Asano, a 16-year-old girl who requests Manji's assistance in killing those who slaughtered her parents. Initially reluctant, Manji refuses Rin's desperate plea. However, owing to her evident lack of strength, Manji changes his mind and agrees to protect Rin for four years. With this partnership set in stone, the two embark on a perilous journey of bloodshed, vengeance, and redemption, each to fulfill their own life's cause.

Despite their distinctive personalities, Souma Shiki, Hayate Ichikura, Shun Futami, and Takayuki Mima all have one thing in common: though naturally clumsy, the four disguise their embarrassment from tiny slip-ups by maintaining a composed demeanor. However, it is actually the guys' airheaded natures that makes the girls' hearts throb. No matter what happens in their daily lives, the boys do their best not to lose their cool!