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.
The F City Department of City Security gains a new member in the form of Ropponmatsu, a female android bomb disposal unit who becomes a new love interest for Iwata. However, Ropponmatsu will be put to the ultimate test when ACROSS delivers a bomb in an alley.
A second Ropponmatsu unit appears, but this time in the form of a young, irritating cat-girl who gets on everyone's nerves. Moreover, when a second bomb appears in F City from ACROSS (disguised as a panda no less), it is up to Ropponmatsu 2 to save the day.
A shipping error lands prototype versions of Ropponmatsus 1 and 2 into Excel's and Hyatt's care. Upon arrival, the two female androids fall in love with the ACROSS agents, causing much chaos, pandemonium, and hilarity.
Ilpalazzo sends Excel and Hyatt to investigate the United States where they stumble upon the anime mafia, who had gotten Pedro's son, Sandora, involved. Excel saves the day, using the conventions of Japenese and American animation, including a vaguely familiar magical girl parody.
In an attempt to secure the city, Kabapu dresses his Department of City Security in Power Ranger-type outfits equipped with new powers. The department then wreaks havoc on F City fighting crime, even the tiny, insignificant ones.
Key, a visually appealing musician, arrives at the ACROSS base to deliver (or rather sing) a message from ACROSS HQ to Lord Ilpalazzo. However due to lack of inspiration, Key is unable to deliver the message. Frustrated (and jealous), Ilpalazzo orders Excel and Hyatt to look after Key until he is able to deliver the message.
The Puuchus are back, and this time they mean business! In a nod to Leiji Matsumoto, as well as the Gundam series, the Puuchus wage war over the invasion of Earth, and Excel is caught right in the middle of it!
When F City falls into ruin due to the events of the previous episode, law and order cease to exist and powerful gangs rule the barren wastelands. It is up to Excel to restore order back into the chaos. Little does she know that there is a sinister plot to do her in for good, from the last place she would expect.
In an episode devoid of humor (as per Koshi Rikdo's orders), Excel suffers amnesia from the deep trauma received from the previous episode, Ilpalazzo tries to come to terms with the decisions he had made, and the Department of City Security vows to stop ACROSS, once and for all.
Il Palazzo has gained superhuman strength, and battles both the Daitenzin and Excel, who is seeking answers after regaining her memory. Meanwhile, Pedro, Sandora, Nabeshin, and his fallen comrades face off against That Man in a final battle.
Cossette returns as the third member of ACROSS, and gives Excel and Hyatt a potion which causes the two to switch bodies. This results in hilarious hijinks, as Watanabe takes Hyatt (in Excel's body) to a love hotel, and Excel (in Hyatt's body) adjusts to a far weaker body. Meanwhile, Nabeshin chases That Man's clones, and Il Palazzo plays guitar with the Mohawks on his three day break.