In the backwater town of Bellforest lives a 14-year-old boy named Renton Thurston. He desires to leave his home behind and join the mercenary group known as Gekkostate, hoping to find some adventure to brighten up his mundane life. However, stuck between his grandfather's insistence to become a mechanic like him and the pressure of his deceased father's legacy, the only excitement Renton finds is in his pastime of riding the Trapar wave particles that are dispersed throughout the air, an activity akin to surfing. Everything changes when an unknown object crashes through Renton's garage, discovered to be a Light Finding Operation—a robot capable of riding the Trapar waves—specifically known as the Nirvash typeZERO. Its pilot is a young girl named Eureka, a member of the Gekkostate, who requests a tune-up for the Nirvash. Their meeting sparks the beginning of Renton's involvement with the Gekkostate as he takes off alongside Eureka as the co-pilot of the Nirvash.

In a post-apocalyptic world, the last remaining human settlement in Japan is the heavily fortified city of Tokyo-3. Fourteen-year-old Shinji Ikari is brought to the headquarters of NERV, an underground organization lead by his estranged father, Gendou. He requests that Shinji become a pilot of an Evangelion, a colossal android built to fight against monstrous and destructive alien creatures known as Angels that wreak havoc on the planet and threaten the survival of the remaining human race. Although initially reluctant, Shinji is swayed by the idea of reconciling with his father, and agrees to aid in mankind's perilous endeavor against its alien threat, as the pilot of Evangelion Unit-01. Thrust into the midst of a dangerous battlefield, Shinji must find the necessary courage and resolve to face against the Angels' incursions before it is too late.

When the threat of the Angel menace escalates, mankind's defense force is pushed to its limits, with NERV at the forefront of the struggle. Shinji Ikari and his partner Rei Ayanami are assisted by two new pilots: the fiery Asuka Langley Shikinami and the mysterious Mari Illustrious Makinami. With the aid of their mechanized Evangelion units, equipped with weapons perfect for engaging their monstrous opponents, the four young souls fight desperately to protect their loved ones and prevent an impending apocalypse. But when startling secrets are brought to light, will the heroes' greatest challenge prove to be the monsters...or humanity itself?

It is hard to take over the world, and the enigmatic Il Palazzo, head of the ACROSS organization, knows this, so he aims to start small by conquering the city of Fukuoka. Two young officers, Excel and her partner Hyatt, are tasked with executing this plan, but standing in their way are the City Security workers, a group consisting of three mostly normal guys, a very severe girl, and some robots. Regardless of simplicity, Excel and Hyatt always manage to screw up their missions, which usually result in death and lots of destruction. Heppoko Jikken Animation Excel♥Saga chronicles the elaborate troubles that the ACROSS officers get themselves into, as Excel and Hyatt never fail to do their jobs improperly.