Excel becomes an agent of the secret ideological organization of ACROSS, whose plan is to conquer the corrupt world (or at least F City) and remake it in its own image. Lord Ilpalazzo, ACROSS' leader, orders Excel start the conquest by exterminating the world's manga artists starting with Koshi Rikdo, the original author of the Excel Saga manga.
In the style of a dating simulation game, Watenabe, one of Excel's next door neighbors, falls in love with Hyatt and takes her out on a date. Meanwhile, Ilpalazzo is shown playing a hand-held dating simulation game which is apparently influencing Wantenabe's actions.
Ilpalazzo sends Excel and Hyatt on an excursion to the mountains to set up lasers pointing towards F-City. Meanwhile, Wantnabe, Iwata, and Sumiyoshi (Excel's next door neighbors) join the F-City Department of City Security where they meet Misaki Matsuya, an attractive, but fierce red head.
Excel and Hyatt try to divert The Department of City Security's investigation of a sewer that leads to ACROSS' secret base. However, the return of those (not-so) adorable Puuchus may screw up everybody's plan.
It's girls day out as all the female characters chill out at the neighborhood pool while the guys remain off-camera. Excel and Hyatt meet up with a cute 8 year old named Cossett Sara, who actually hides dark secret.
Excel and Hyatt investigate the Japanese education system by going undercover as teachers at Excel's old high school. While at the school, the two are charged with the task of managing the school's baseball team in their upcoming match against a rival High School.
The F City Department of City Security shadows a young, cute (yet possessed) female detective, trying to solve the mystery of her father's murder. Meanwhile, Hyatt gets kidnapped by a couple of bumbling robbers.