S03E01
When Eugene finds out that Johnny is what stands in the way of him and Susan, he sets out to lock Johnny up forever as he tries to get the last ingredient for his sister's "Susan-hating lozenge".
S03E02
Johnny wants to buy an HDTV and the twins need an important ingredient for their experiment. The only solution: Enter Johnny in a professional wrestling competition so they can win $10,000, so they make Johnny a wrestling suit which allows him to spray stink gas from his suit.
S03E03
Brain Freezer creates an army of snowmen, and only Johnny X can stop him.
S03E04
After Johnny and Dukey send Bumper packing, they start to come against each other in a game of "Say Uncle".
S03E05
Fed up with the lack of respect, Dukey has convinced Mary and Susan to turn Johnny into a dog. In the meantime Mary and Susan turn themselves into animals so they can get loved by Gil. It all goes wrong when Animal Control arrives and snatches them.
S03E06
After hearing about American heroes in Social Studies class, Johnny decides to help his classmates by bringing back applesauce as a vigilante after the Lunch Lady outlaws it. However, this lands him into trouble.
S03E07
Johnny and Dukey are transported into their favorite video game, Tiny'Mon, but they end up trapped and must defeat Blast Ketchup, and his Tiny'Mon Kadoomerang, to get back home, with only the seemingly useless Cuddlebuns for protection.
S03E08
Johnny refuses to bathe, and his family forcibly attempts to wash him. Meanwhile, Dukey is mad because he thinks Johnny forgot his birthday.
S03E09
Mr. Black and Mr. White ask Susan and Mary to design a new weapon, so they make a helmet that allows the user to control things with their mind. But it becomes a huge mistake when it's stuck on Johnny's head, and his obsession with a new video game now makes any inanimate object he sees turn into a monster.
S03E10
Johnny is upset because the holidays that give free candy to the world are spread too far apart, so Johnny decides to start his own holiday, known as Kids Get Free Candy Day, and try to spread free candy. When there are some adult protests against this holiday, Johnny, Dukey, Susan, and Mary gain an unlikely ally against this – the Beekeeper.
S03E11
When Dukey explains how narration makes everything seem better, Johnny convinces Susan and Mary to make a reality warping megaphone, but it malfunctions.
S03E12
Johnny buys a video game which turns out to be a military plot to recruit an elite team of super soldiers, and then he must join the fight against a group of renegade penguins who are losing their home to global warming.
S03E13
Johnny drinks an unstable isotope so he can get sick and not have to study for a test for school. Unfortunately, not only does the isotope give him red spots and a purple tongue, if it's not cured within four hours, it's going to give him immense bloating, cause violent coughing, and eventually make him explode.
Johnny has his sisters use an invention that will give him a mustache so that Johnny can get into a movie meant for older people. But when Bling Bling Boy pesters Johnny to use the invention on him, Johnny shoots the invention at him too much and now Eugene looks like the monster from a movie.
When Bumper uses kung fu moves to take over the school, Johnny seeks Dukey's kung fu advice, but to no avail.
Bling-Bling Boy steals Susan and Mary's shoes, and it is up to Johnny and a reluctant Dukey to retrieve them before their dinner with Gil.
Susan and Mary need to get Lolo away from Johnny and Dukey for various tests when they try to make a profit out of her in order to get a video game system.
Johnny must make a bench for woodshop class or he goes to summer school.
Doggone doggy adventures result when Susan and Mary fashion a mind-controlling obedience collar to tame Dukey's bad behavior. Then, the girls invent an acne cream.
While trying to find life on other planets, Johnny meets a leader from the planet Vegandon who attempts to destroy the Earth by sucking out its natural resources.
All Johnny and Dukey want is a simple bike race between the two of them; but everyone joins the race.
Johnny and Dukey test a perfume experiment and now everyone is attracted to them. They use this to their advantage, but it goes out of control.
Seeking revenge, Blast Ketchup sucks Hugh into the Tiny'Mon world, trying to suck Johnny in. Thinking he is one of Johnny's Tiny'Mon, he captures him. Johnny, Dukey, Susan, and Mary must stop him. To re-exit the game, they must win another battle with Blast.
When a condemned hotel gets haunted by ghosts Susan and Mary drag Johnny, Dukey and Gil into the house to prove that the ghosts are fake.
It's time for the Earth Day Carnival and the Johnny Stopping Evil Force 5 (with Zizrar replacing the Beekeeper) returns and obtains the same mutant powers as Johnny X, and Super Dukey.
Following the events right after "JX6-a: A New Beginning" Dark Vegan returns to destroy the Earth with an upgraded armada. Dark Vegan, with his upgrade armada, is cutting up the Earth's trees, taking off the oxygen and sucking up the Earth's water. Johnny, Dukey, and the Johnny Stopping Evil Force 5 team up to stop Dark Vegan and return the Earth's resources.