Red Guy is trying to know the secret identity of Supercow.

Mom and Dad send Cow and Chicken to military school to teach them discipline, but are appalled when they return as iron-minded machines.

Cow and Chicken go to the arcade, and play the time machine. They find themselves back in a deserted time, where The Red Guy introduces them to the primortial soup. But when Cow accidentally drops her quarter into it, everyone in the present time has quarters for heads. Cow and Chicken must go back into time again to stop her.

Cow learns that she has a herding instinct, and soon starts to fit in with other crowds such as flocks of ducks, schools of fish, and the military. She soon learns that she is supposed to herd with other cows, so she does, but soon dislikes it when all the other cows do nothing but stand and eat grass.

Cow and Chicken both win a contest that allows them to spend a day in the career of their choice.

Mom and Dad decide to let Cow have a pet. She choose an anaconda, after it eats Chicken, and she hears his voice from inside the snake, and assumes the snake can sound just like Chicken. Cow names the anaconda, Fluffy, and Fluffy soon grows attached to Chicken, as its full-coarse dinner.

Chicken, Flem, and Earl play a game of kickball. Cow's udders kick the ball into the bushes, where Chicken, Flem and Earl discover a laughing puddle. After Flem and Chicken run back out, they forget the ball, and go back to discover that Earl is in the puddle. Chicken sends Flem after him, and he is stuck too. Chicken then gets Mom and Dad, who jump into the puddle, and Chicken drops Cow in there to save everyone. Chicken is then the only one left, until he discovers the puddle is a doorway to Boneless Chicken's nightclub.

The Red Guy is now Captain Butz Pirate, and wants to give Cow and Chicken pirate lessons. He takes them aboard his pirate ship in the middle of the duck pond, and teaches them how to say ""argh"", carve peglegs, hold worms for ransom, and sink Flem and Earl's boat. But after that incident, Cow, Chicken, and their flag/man Jolly Roger declare mutiny.

The Red Guy hosts a new late night talk show called ""Dead Ghost, Coast to Coast"", and reminds the viewers that tonight's Halloween. Chicken calls in, and is instructed to dress as a human being. So, Cow and Chicken go trick or treating as Mom and Dad, only to find that the neighbors assume that a grown man and woman are trick or treating. With that, Super Cow and Chicken teach The Red Guy a lesson.

Cow's tongue rips out of her mouth and runs away. He then causes havock all over town, by hi-jacking someone of their motor-scooter, rolling around in someone's gravy, and licking the candy store dry. Soon, Tongue finds himself on the lam, and runs back to Cow. Everything is back to normal, until Chicken's wattle decides to run away to.

Chicken is tired of always having to do chores, so he chews Mom and Dad out, and runs away to be a bachelor with Cousin Boneless Chicken. One at Boneless's Chicken attracts the attention on Boneless's blind-date, Linda. Linda falls head over heals for Chicken, which makes Boneless disgusted.

Cow, Chicken, Flem, and Earl try out for the school's sumo wrestling team. For being big and fat, Cow is the new team member. Soon, everyone fears her, and she feels degected, but it benefits Chicken, because now no one will beat him up.

Cow and Chicken's class go on a field trip to the Cometorium, where Chicken is bored stiff. After getting hit by one of Dad's golf balls (he was golfing right next door), Chicken hangs it in front of the telescope; soon, the whole town is in panic of the arrival of ""Dad's Ball Comet"".

Cow, Chicken, Mom, and Dad go on a safari in Africa, where they run out of gas. Cow and Chicken then find themselves at the mercy of laughing hyenas, and man-eating giraffes. Super Cow comes to the rescue, only to find that she has actually been defeated by the Grizzly Beaver, who has eaten the giraffe, who has eaten Chicken.

A group of female bikers break into Cow and Chicken's house, and start gnawing on their carpet. One of the bikers has a crush on Cow, and invites her to join the Buffalo Gals. It's up to Chicken to save his sister.

The Red Guy is depressed because no one will play with him. After seeing Cow has Crabs the Warthog, he wants to play with her because he has Crabs's doll house. When he askes to play with Cow, she tells him not if he was the last man on earth. With that he locks the entire world in a trailer, and is the last man standing: but Cow still won't play with him.

Cow has a crush on Crag, the smartest kid in school, but is ignored by him. Her friends try to convince her that her horns are too small, so she tries every way to make them bigger by decorating them with coat hangers, paper masche, and even chocolate chip weenies. Cow later learns that Crag wasn't interest in Cow, because he had a crush on one of her friends.

While driving in the snow, Mom and Dad find The Red Guy who says he's heading ""home""; so Mom and Dad take him home with him, and immediately think of him has their new favorite son. Cow and Chicken work together to try to prove The Red Guy's a fraud.

Cow is depressed because she has no friends: until she finds a fly in her room and befriends it. Pretty soon she and the fly are inseperable: until Chicken, Mom and Dad call in the fly exterminator.

Cow and Chicken get an unexpected visit from Cow's twin cousin, Sow (a pig with 8 teets). After Sow's first day at school, she causes chaos, and puts the blame on Cow. It's up to Cow to pull the plug on Sow's evil ways.

Cow brings home an ""invisible"" dog, whom she dubs, Kevin. Pretty soon, she and Kevin are inseperable, but causes trouble with school and friends. After she enters Kevin in a dog show, and wins, Kevin ""runs away"". Afterwards, Cow finds Kevin, befriended an ""invisible"" homeless man.

Grandma pays at visit to Cow and Chicken's house to take them to the mall with her. Her purpose for being at the mall: to look for a new grandpa, because she lost the old one. Chicken gives her the slip while he, Flem and Earl hang out at the concession stands.

Chicken refuses to take bath, so he just sits there in the empty tub, while Cow, Mom, and Dad try to make him take a bath so they can use the toilet.

Cow and Chicken are taking a trip all by themselves. Their taking an airplane. Once Chicken sees the actual plain, he starts to have anxiety attacks and believes that flying is a dangerous way to travel.

Chicken tells Cow that she's not artistic, so she in return, sculpts a seal out of a stick of chewing gum, and an entire machine full of bubblegum balls. Cow wishes that her chewing gum seal, whom she names Chachi, was real. Suddenly, a wishing star grants her wish, and Chachi is a real, miserable, ho-hum seal.

Everyone makes fun of Cow because she still has her old security blanket. She then tosses it out the school bus window, but is depressed for the rest of the day. Chicken tries the cheer her up by playing the bad guy in a game of Super Cow. Cow confesses that her blanket was also Super Cow's magic cape, and that Super Cow was never coming back. Red Guy then sees the perfect opportunity to torture Flem and Earl. Chicken decides it's ""Wonder Wattle"" to the rescue.

Sick of their everyday life of being squirted with milk, Cow's favorite toys: Crabs the Warthog Doll, Piles the Beaver Doll, and Manure the Bear decide to run away to find their original owner. After reading Manure's tag that says ""Made In Hong Kong"", they assume their original owner is a maiden named Hong Kong, and set out on a quest to find her.

Cow and Chicken wait outside the hardware store while Dad shops. Chicken is dying to ride the fighter jet plane ride. When Cow finally lends Chicken a quarter, The Red Guy takes the ride away. Chicken then stows-away on his truck, to ride the plane, but has to plug it up. Once at the gas station, he buys 20 extension cords, but the owner unplugs them. In the end, Chicken discovers that Dad actually collects those kind of rides.

It's ""Bring Your Kids to Work Day"", so Dad does just that. Dad's job is guarding the government's money. When he has to appear at a sudden confernce, he leaves Cow and Chicken in his office. Red Guy, who is now a Canadian Mounty Police, finds them, and begins to stalk them, until they surrender.

Dad loves shopping for Mom's stuff. He runs off to get a manicure for her, while Cow and Chicken pay for the other items. The censors go off when Cow passes through, so Red Guy, as a mall cop, chases Cow and Chicken all over the store. Cow learns that the censors have been broken for weeks. Red Guy walks through, and is arrest by the REAL mall cops.