Ilpalazzo quiere exterminar los artistas de manga del mundo y ordena a Excel comenzar con Koshi Rikudo, pero ésta es afectada por la intervención de la Gran Voluntad del Macrocosmos y su propia consciencia. Luego de conversar con Pedro, un trabajador inmigrante, y de capturar su cena, Excel hace un segundo intento para terminar con la vida de Rikudo.

Unos refuerzos del cuartel general de ACROSS son atacados en una invasión por los seres de dulce apariencia llamados Puchuus. Excel ataca su madre nodriza. Mientras tanto, Nabeshin se encuentra a bordo para salvar a un viejo amigo y escapar de los Puchuus. Al final, la fuerza invasiva extraterrestre es destruida, Excel es capturada como prisionera de guerra e Ilpalazzo admite a Hyatt dentro de las fuerzas de ACROSS.

Como si fuese una película "Clase B", Excel está atrapada en la jungla. Hyatt es enviada para hallarla y se encuentra con su vecino Watanabe en la trayectoria. Los captores de Excel son tropas de hombres muy varoniles y grandes (con un punto débil por los perros) pero Nabeshin tiene algunos asuntos pendientes con ellos y con el compañero de encierro de Excel.

En una parodia a la comedia romántica en el anime, Watanabe se interesa por Hyatt y sus pensamientos son reflejados en las opciones que ofrece un juego de simulación de citas. Pero el destino e Ilpalazzo juegan con él. Mientras, Excel busca a Hyatt y ambas son capturadas.

Excel y Hyatt se infiltran en el Ayuntamiento para darle su merecido a los políticos corruptos. En el curso de sus investigaciones, se encuentran con el Dr. Kabapu, quien controla a los líderes de Ciudad F y no tiene miramientos en usar la violencia para conseguir sus objetivos. Kabupu crea el Departamento de Seguridad Civil con fondos malversados y contrata a Watanabe, quien sueña con un trabajo en el gobierno tanto como Iwata y Sumiyoshi. ACROSS triunfa de algún modo, con la ayuda de zombis y unos garabatos que aparecen en los baños.

ACROSS planea construir un láser en las montañas para aterrorizar y amenazar a la Ciudad F. Mientras tanto, Watanabe, Iwata y Sumiyoshi son enviados a un ejercicio de entrenamiento en las aquellos lugares en donde conocen a su nuevo compañero de tareas, la audaz y sensual Misaki Matsuya, quien se convierte en el nuevo objeto de deseo de Iwata.

When Kabapu sends Watanabe and his colleagues to investigate the sewers surrounding the Across base, Ilpalazzo dispatches Excel and Hyatt to deal with the intruders. However, even as the duo familiarise themselves with the Across security system, they discover a far more sinister breed of intruders lurking in the sewers- an army of Puchuus led by the nefarious Puchuu Queen! Will Excel and the others be able to stand against this overwhelming cute force of evil?

It’s an all-girl fan service fest as Excel and Hyatt take off to the swimming pool, accompanied by local girl Cosette. But even as they laze in the sun and enjoy all the clichés of a summer episode, it appears that Cosette may have a deadlier mission in mind than simply taking a quick dip in the pool. Could such a cute little girl really be a sinister assassin? On a show like this, anything seems likely…

When Ilpalazzo orders Excel and Hyatt to learn how to control the masses through their most popular sports, the duo end up working in the rather less than mainstream field of ten pin bowling! However, what looks to be nothing more than a quiet part time job in a bowling alley soon becomes far more dangerous when the alley is taken over by an evil terrorist group of middle-aged bowling fanatics! Now only woman stands in the way of these miscreants—the over-energetic yet under-competent Excel Excel…

When the stress of life as an emergency food supply becomes too much for Menchi, she takes the first opportunity she can to escape from Excel’s apartment and go in search of her former owner, a kindly old man. Life on the streets soon proves quite tough for the little dog, however, but fortunately help is at hand when she meets up with a disparate gang of dogs all conforming to well-known movie stereotypes. With her new friends by her side, Menchi continues her quest for the old man, but in typical fashion, danger and betrayal are lurking around every corner…

Thanks to the state of modern education, the future is looking bleak—and that means that Across must take action. To that end, Ilpalazzo sends Excel and Hyatt to work at Excel’s old high school, which has since become a dumping ground for all manner of juvenile delinquents. But no sooner have they tamed the students than a new challenge arises—whipping the school’s woefully poor baseball team back into shape. But even with all the clichés of sports anime on their side, will Excel and Hyatt be able to create a team good enough to win their crucial match against the Monkey Balls High team?

Having decided that his employees need some additional training, Kabapu sends Watanabe and the others to train under Purin, a detective who can turn from a tough-as-nails old-timer into a cute girl quite literally at the drop of a hat! And whilst they tag along for Purin’s latest case, Excel has some problem solving of her own to do when Hyatt is taken hostage by a pair of burglars.

It had to happen eventually. The producers got behind schedule—there’s way no way enough material for a whole new show could be produced in time. So what plan than to polish off some old clips, do some fancy editing, and make up a review episode? Yes, it’s Excel Saga’s turn for a clip show, framed by a seasonal New Year-Year’s End Hidden Talent Content, as presented by Excel and Hyatt.

In order to pick up flagging ratings, the Excel Saga writers introduce a new character: the android lady Ropponmatsu, creation of Dr. Shioji, a brilliant scientist with a mostly-innocent (thank goodness) fixation with small girls. Iwata, of course, becomes hopelessly enamored with Ropponmatsu, completely clueless to the fact that she’s not a living, breathing human. Meanwhile, Excel and Hyatt manage to bungle a seemingly simple mission to deliver a package with a bomb in it, one discovered and disarmed by Ropponmatsu… well, not quite, much to Iwata’s horror.

Menchi makes another break while Excel and Hyatt are out of town on a mission, and ends up on a boat to America. There, she meets Ann Anzai, a young lady who must travel the world in 80 hours before she can collect her inheritance from her grandfather, and accompanies the girl on her adventure. Can the two of them make it in time, and can Menchi defend her new friend from a mysterious assassin out to get both of them?

Annoyed that Ropponmatsu has bought it after only one episode, the merchandising team demands that she be put back in the show immediately. In the meantime, Iwata tries to put up with Ropponmatsu 2, an annoyingly cute little-girl version of the original Ropponmatsu, and Excel and Hyatt try their last mission over again, this time with a robot of their own!

After getting demolished again in the last episode, new copies of Ropponmatsu 1 and 2 are delivered to Watanabe’s apartment. But by mistake, Excel and Hyatt accidentally activate the new models, which immediately become fixated with them, in more ways than one! But will this double dose of shoujo-ai end in tragedy… or just dark comedy?

On a mission to investigate the situation in America, Excel and Hyatt run into a band of street thugs… and a communication problem. Fortunately, they get some help from Sandora, the son of Excel’s late friend Pedro, who is working as a cel animator to support his mother. But it seems these cels are being hoarded by an evil gangster, who quickly gets a hard lesson in the rules of cartoon heroics by an outraged Excel.

Desperate for more material, the writers of "Excel Saga" take a page or two from Koshi Rikdou’s old "masked heroes" parody Daitenjin, and have our hapless heroes in the Safety Assurance Agency (Watanabe, Iwata, Sumiyoshi, Matsuya, and both Ropponmatsus) made into the Municipal Force Daitenjin, against their will no less. In order to get out of the rather uncomfortable jumpsuits, the team goes about finding and dealing with all the terrible crimes (or not-so-terrible ones) they can find.

Having charted the misadventures of Pedro, as he struggled for a season and a half to return home to his son and his sexy wife, the writers of Excel Saga have Excel and Hyatt sitting around in a bar and recapping Pedro’s escapades. Yep, it’s another clip show… but with a twist, as new footage is revealed showing the return of Nabeshin, and the kidnapping of the Great Will of the Macrocosm and Pedro’s wife by the evil That Man!

Fed up with Ilpalazzo’s lack of progress, ACROSS HQ sends the leather-clad, ruggedly handsome, and more-bishonen-than-thou agent Key to deliver an important message to Ilpalazzo. But rock-star wanabee Key, being the "artise" that he is, won’t deliver his little singing telegram until his muse returns. In the meantime, an envious Ilpalazzo sends the lovestruck Excel and the blasé-as-usual Hyatt to keep an eye on Key. That’s easier said than done, though, as Key hooks up with a down-on-their-luck "visual-type" band and turns them into superstars, even scoring them a big gig, where he plans to reveal his big message on national television…

Having finally gotten the hint from ACROSS that he should hurry up the whole invasion thing, Ilpalazzo orders Hyatt to perform final preparations for the conquest of the city of "F", and orders the bungling Excel to keep her nose out of it. Excel has no time to be dejected, though: the Puchuus have returned, and she and Hyatt must help a band of freedom fighters thwart the machinations of an evil conqueror and his really big spaceship! But even after our favorite ACROSS agents defeat the invaders and destroy their ship, the city of "F" gets squashed by the falling debris. Well, them’s the breaks…

We find Excel wandering the wasteland that once was "F" City, where she becomes entangled in a conflict between a settlement of survivors and a band of maraudering raiders. After fending off the thugs with her "ACROSS Martial Arts" (which involves beating the opponent in the right places ’til they turn into a Digi Charat character), Excel finally finds her beloved Ilpalazzo… only for him to strike her down callously. Without the Great Will to ressurect her, can the mortally wounded Excel survive? (She’d better, the series isn’t over yet!)

After Koshi Rikdo declares this episode to be gag-free, an amnesiac Excel gives the performance of her life after being rescued by the surviving members of the Safety Assurance Agency (i.e. all of them). But as she copes with her betrayal and tries to recover her identity, Ilpalazzo is having an identity crisis of his own, as his drive to conquer pushes him further forward. Angst and pointless plot twists abound as Excel searches for ACROSS… and Ilpalazzo struggles with his ambition.

Fed up with the insanity, Koshi Rikdo finally insists that the animation and writing crew finish the freaking series already. So, the Safety Assurance Agency locks horns with ACROSS, Excel tracks down Ilpalazzo and beats some sense into him, Watanabe finally realizes the truth about Hyatt, and the series finally comes to an end… or does it?

In this aptly-named epilogue, an aborted attempt at making a musical version of Excel Saga is replaced by an exercise in pushing the boundaries of good taste for even Japanese television. As a small sampling of the insanity, Excel and Hyatt (the former more deranged than usual, the latter more sickly than usual) switch bodies, Cosette returns only to get naughty with Dr. Shioji, Watanabe takes Hyatt (in Excel’s body) to a love hotel, Nabeshin gets married, and there’s way too much blood and pointless violence. What better way to end a "Quack Experimental Anime"?