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.