This season has 13 regular episodes.
This season marks the first appearance of the three nerds of the Secret Snake Club, a school club dedicated to snakes and their dark powers. Also appearing are Thromnambular, a mysterious talking skull that grants wishes; Wiggy Jiggy Jed, Billy's ideal pet, made from magically combining four dogs; an Invisable duck that makes farting noises; Principal Goodvibes, the friendly but boring principal at Billy and Mandy's school; Daisy, a chupacabra that steps out from the TV while watching a videotape; and Dracula, the senile king of the vampires, now living in a retirement home. Minor characters that would later recur are Judge Roy Spleen, and Irwin's grandmother, Tanya.
Recurrent characters that are also featured include Harvey, Bride of Fankenstein, Wolf Man, Scythe 2.0, Sassy Cat
At school, Billy, Mandy and Irwin look for a club to join. Irwin plans to join the Macrame club in order to meet girls; Billy inquires on the Junior CIA club, which forcefully recruits him; Mandy joins the "Secret Snake Club", a snake-themed club consisting of three geeks. In their headquarters, the nerds reveal that their "secret agenda" is to resurrect Shnissugah, a giant snake which lived hundreds of years ago in Canada, to take revenge against the popular kids, but they lack the power of the Underworld to do so. Then, Mandy calls for Grim, who proceeds to revive Shnissugah through the internet. In the end, Billy, as a junior agent of the CIA, stops a criminal plan by Irwin, who was using the Macrame club for personal gain; and Shnissugah turns out to be a tiny, 8-cm (3.14-in) long, harmless snake.
When Billy and Mandy's school is preparing for a big game, Mindy entrusts the care of the school's mascot, Fluffy Cat, to Billy, to protect him from being kidnapped by the rival team, the Booty Heads. Then, at Billy's house, Fluffy Cat is a disaster, so Billy's mom throws him into the basement, where the cat gets inside Grim's trunk, absorbing its powers. In the end, a giant Fluffy Cat appears just before the game wreaking havoc.
As Billy is tired of all the rules in his house, he can't resist the urge to try his father's new motorcycle. As expected, the motorcycle breaks down and Billy asks Grim to repair it. However, Grim's scythe turns the motorcycle it into a wild, supernatural vehicle, which in turn transforms Billy's parents and everyone else around it into undead creatures and motorized monsters. In the end, Mandy makes Billy tell the truth about breaking the motorcycle in the first place, at which point his parents and everyone else return to normal.
After Billy's baseball team loses badly against Mindy's, Grim decides to coach them. Mandy is not allowed on the team, as Billy is reluctant to let girls play, although he doesn't realize Mindy is a girl too. Then, Mandy puts on a baseball cap and, assuming the role of "Manfred", pitches for Billy's team anyway. With additional help from ghoulish players which played in the Underworld Little Leagues alongside Grim, Billy's team wins when Pud'n hits a home run.
While at Sassy Cat Land, the theme park dedicated to Sassy Cat (and to ridiculously long queuelines), Billy, Mandy and Grim stumble upon a closed attraction, a futuristic "house of tomorrow". Inside, they find Master Control, an intelligent computer claiming to know everything (and wishing death upon the trio when Billy angers him), and Tom Smith, a tour guide that became trapped in the house when it closed 40 years ago. Tom explains that the attraction closed when a kid, actually Billy's dad, annoyed Master Control with his dumb questions, and the robots started attacking the humans. In the end, Billy, Mandy and Grim exit the house unharmed, but Tom misses his opportunity to escape and is left behind again.
After a trip to the mall, Mandy becomes the spokesperson for Happy Huggy Stuffy Bears, a new stuffed toy in town. After the success of her commercial, Mandy gives away stuffed bears to other children, who then start wreaking havoc in the city. As it turns out, Eris, the goddess of chaos, is behind the toys, which mind-control the children into creating chaos. In the end, Mandy decides not to share control of the world with Eris, and orders Grim to destroy the toys.
When Billy finally gets a "secret decoder ring" in his Blasto Bits cereal, he receives a holographic message from a strange creature who speaks about finding the "Secret of the Universe" in an abandoned mine shaft. Then, all the other children of Endsville, also with decoder rings, race to the mine to be the first one to get the Secret. In the end, the entire effort is revealed to be a trap laid by Lubbermouth, a worm-like creature from Grim's past, who wishes to free herself from the curse of guarding the Secret. Then, when Mindy looks down at the pit, she becomes the new guardian of the Secret and has to stay there forever.
One night a strange odor travels through the city, prompting the noses of all the people, including Billy's, to follow it. The next night, Mandy, who is noseless, and Grim decide to wait outside Billy's house for the event to repeat. Then, when the odor reappears, the nose parade leads them to the shopping mall, where they meet a "Nasalmancer", a nose wizard, who is trying to take over other people's noses since he lost his own. In the end, Billy recovers his nose, but slices it in two, and gives one half to the Nasalmancer.
When Billy goes into the mud for the fifth time in the day while wearing his white tuxedo before a wedding, Grim tries to figure out why Billy is so stupid, in other words, what is his "problem". Then, Billy's dad, Harold, recounts Billy's life from his birth until he met Mandy, and explains that Billy is not dumb, but actually a genius with a certified "Honorary Genius Degree". In the end, it is quite evident to Grim that Billy's problem is his equally dumb father.
After Grim's robe comes out of the washing machine, Billy and Mandy find Thromnambular, a talking skull with ruby eyes and a number nine imprinted on his forehead. Then, Grim tells them that the skull is a magical artifact imprisoned on Earth that must grant his nine wishes in order to be free. When Mandy asks Grim why he hasn't used any of the wishes, Grim tells her that the skull will corrupt the wishes and end up affecting the wisher. Despite this, Billy runs away with the skull and makes the first wish: (1) he wishes to be in an adventure (which parodies Indiana Jones and Jonny Quest), this backfires because Irwin is eaten, which Billy complains about getting him in trouble. After this, Thromnambular is found by different people who each make a wish: (2) Billy's dad wishes he could live again his High School years, but this backfires because he is not popular; (3) General Skarr wishes to rule on high, but this backfires because he asphyxiates in space; (4) Irwin (despite being eaten already in an earlier episode) wishes he was in a Hip-hop video, but backfires because he gets punched by Mandy; (5) Pud'n wishes he had a bunny, but he is attacked by it, because "Sometimes Love Hurts"; (6) Nergal Junior wastes his wish by wishing to know what to wish for; (7) Sperg wishes for a way to get into the girls restroom, in order to bully a girl into giving him a large sack of money, this backfires because he is turned into girl, and then insulted by the other girls for being ugly; (8) Mindy wishes to be a "big star", but this backfires when she is sent into space strapped to a rocket; (9) finally, Mandy tries to auction the last wish, but Grim gets ahead and wishes the kids never found the skull in the first place. This then goes back to the beginning of the episode where Billy is staring at the washing machine, followed by Mandy pushing him into it.
When Billy gets the opportunity to adopt one of four dogs, he says he wants them all. Then, Grim uses his scythe to magically combine the dogs and create Billy's dream dog, who calls himself Wiggy Jiggy Jed. Although initially Billy and Jed are best friends, their relationship falls apart when Billy tells Jed to sleep outside. In retaliation, Jed uses the powers of Grim's trunk to build a giant machine to capture the beds of all people. In the end, Billy throws Jed a dish of primordial ooze and he dissolves.
In order to raise money to buy Sea-Critters (similar to Sea-Monkeys), Billy has a garage sale where he sells Grim's scythe to Irwin for less than two cents. Then, with the power of the scythe, Irwin hypnotizes Mandy and takes her on a date. Later, Billy and Grim try to recover the scythe, and when they do Mandy gets out of the trance. In the end, Irwin is punished by being transformed into a Sea-Critter and placed in Billy's fish bowl.
When Billy gets under his house's foundation, he encounters again his "son", Jeff the Spider, who has just laid eggs. Then, Jeff tries to make things right with Billy so he can take care of the baby spiders, as he is going to die after the eggs hatch. Naturally terrified of seeing Jeff, Billy runs away and a wild car chase ensues. In the end, the eggs hatch, and Grim decides to refill Jeff's hourglass that represents his lifetime so he doesn't die, and so he can continue to scare Billy.
After seeing Billy, Mandy and Grim battling a strange creature, Irwin again feels rejected by Mandy. Then, Hoss Delgado, spectral exterminator, appears to help Mandy destroy the monster. Then, Delgado decides to have Irwin as his sidekick and train him to be "cool" in order win Mandy's love. In the following, Irwin gets an attire like Delgado's, and attaches an egg beater to his right hand. Then, Delgado releases a monster so Irwin can fight it and impress Mandy, but he is humiliated anyway. In the end, Mandy tells Irwin he is just a nerd, and Billy tries to assure him that being a nerd is not such a bad thing after all.
After Grim has a nice dream, a nightmare escapes the back of his head in the shape of a supernatural, invisible duck that makes farting noises. Then, the duck follows Grim everywhere, causing him embarrassment with the non-existent farts, and to end up in jail. Then, the duck repeats the strategy, following other citizens, including Irwin and Billy's dad, resulting in all of them going to jail too. Finally, the duck tries to annoy Mandy, but she remains imperturbable by its presence, and eventually the duck disappears and Principal Goodvibes is really super angry to give mandy 75 days of detention.
After being utterly bored of watching the same movie 60 times in a row, Grim takes Billy and Mandy to "Underworld Video" where they rent "The Legend of Chupacabra". While Billy watches the tape, a small, pink chupacabra emerges from his television and Billy decides to keep it as a pet, naming it Daisy. In the end, Mandy and Grim convince Billy that he is inept in taking good care of pets, and they return the blood-sucking chupacabra to the videotape.
Billy and Mandy find a supernatural zipper from Grim's robe, and while Billy uses it to create mischief, Mandy gets herself in a sticky situation.
When Billy jumps into a supernatural puddle (a Cosmic Sinkhole, according to Grim), it takes him to the home of Granny Applecheeks, who wants to bake him into a pie. It's up to Mandy and Grim to save him, if the puddle can take them to right place.
At school, it's time for the "Presidents Fitness Test", but Billy is absolutely unfit for exercise. On the other hand, Nergal Junior uses his shape-shifting powers to become fit at will and excel in every test. Then, Billy asks Junior to transform into a pair of pants that he can wear, so he can run fast and win the 50-meter race. However, since Junior has never attempted to transform into inanimate objects he can't stop running and can't revert to his human form. In consequence, Billy keeps running forever while he becomes a national sensation known as the "Fitness Lad". However, in the end it is revealed that the story was a lie created by the narrator, who parodies The Twilight Zone.
After Grim's scythe fails to open a portal, he decides to sharpen it, but the blade breaks. Then, Billy, Mandy and Grim go to the Underworld to meet "F" (a parody of James Bond's "Q"), who is in charge of the Underworld secret gadgets. Then, "F" unveils Scythe 2.0, an autonomous computerized scythe, that Grim uses while his classic scythe is being repaired. However, when Mandy tells Grim to do his usual humiliating chores, Grim delegates the work to Scythe 2.0, which then rebels and decides to reap by itself, starting with Billy and Mandy. In the end, Grim saves the kids, takes Scythe 2.0 back to the Underworld, and returns with his old scythe.
When Billy buys a new cereal, a phoenix emerges from the box and attaches to his head, annoying everybody. Since the phoenix can't be removed because it revives every time it is destroyed, Billy, Mandy and Grim seek help by going to the factory where the cereal is produced, which is run by Eris, the goddess of chaos. In the end, Mandy tricks the phoenix into leaving Billy and attacking Eris instead. In the end, it is revealed that all the events were really an episode-within-an-episode.
When Billy desperately wants chewing gum at school, Grim gives him a bottomless gumball machine, but warns him not to swallow the gum. Naturally, Billy ignores Grim's warning and starts swallowing the gum, causing him to constantly burp bubbles that fill the entire city. Then, Mandy and Grim try to get Billy to cough the remaining gum that he has in his stomach, but instead Billy swallows the entire gumball machine. In the end, Billy coughs huge amounts of gum all over the city, and ends up with a supernatural rash.
When Billy is accepted to Mrs. Pollywinkle's dancing academy, his father tries to persuade him to forget about dancing because of his own bad experience as a child during a recital. Then, at the academy, it is revealed that Mrs. Pollywinkle is actually a powerful, dark witch set on stealing Billy's soul. Then, Billy's dad unexpectedly comes to rescue, challenging Mrs. Pollywinkle to a dance competition, which he wins using a powerful dance move. In the end, Billy's dad tells Billy to follow his dream of becoming a dancer if he so wishes, but Billy changes his mind saying that dancing is for girls.
When Grim misuses his powers to play bowling with asteroids, he is taken to the Underworld court and sentenced to 50 hours of community service. Then, at a retirement home, Billy, Mandy and Grim go to the supernatural wing, which is the Home of the Ancients, a place for retired, geriatric monsters. There, Grim meets his childhood idols, the Bride of Frankenstein, Dracula and the Wolf Man. Despite Billy's comments that the old monsters are finished, Grim sets out to prove that they are still scary. In the end, Grim tries to scare a bunch of kids in the woods, but the old monsters ruin his attempt and he walks out on them. (Grim is later put on trial for abandoning kids and the elderly out in the woods, who pleads that there is a possibility they may not have been "eaten alive by bears")