The offbeat escapades of unlikely best friends Bill, a rambunctious duck, and Aldo, an alligator from Swampwood, where ducks are usually lunch, not pals.
In parallels to the in-universe TV show “Running Duck,” Bill is almost attacked by Aldo. After finding out that Aldo has a toothache, he takes him to see Cecil, the local dentist.
After Bill starts losing all of his feathers he goes to Bev for help. Getting all but his tail feathers back on, Bill goes into a feather-making machine for a second time, regaining all of his feathers but also turning green.
After dropping a fridge on someone's scooter, Ed, Oly, and Waddle must find a job to pay to get it fixed. After getting fired from Bev's Cafe and several other jobs, Bill asks them to help paint a billboard, but however goes terribly wrong.
Aldo volunteers to be the fifth member in Bill's Squaddo game, but Bill tries to stop him because he hasn't told his family his best friend is an alligator. After eating fried tadpole buttocks, Aldo also gets a case of the giccups (gator hiccups) so Bill and some of their friends try to make the giccups go away.
While using his new telescope Bill spots Aldo in Cecil and Claire's apartment. After being told that Aldo has eaten Cecil and Claire by Ed, Waddle and Oly, they go to the apartment finding that Aldo is only baby-sitting their pet lizard for the weekend.
After Fred the penguin's air-conditioners cause a town power failure, every duck refuses to let him into the pond to cool off. So Bill and Fred go to Swampwood to get some ice and almost get killed while doing it.
Cecil tries to help Bill so he can achieve his dream of learning to fly. After trying over and over again, Bill eventually gets hurt and ends up in hospital.
After being bothered by a fly while trying to sleep Bill decides to go the decoy for a milkshake. He finds Bev tied up by an alligator pretending to be a duck. With Bill and Bev trying their best to get away the fly goes and bothers Aldo to get him to come and help.
Bev starts losing her customers after Waddle creates green waffles that the whole town loves. But after the waffles cause the feathers of ducks to start falling out of them, they quickly go out of business.
After Bill and his friends forget Bev's birthday, she closes the cafe until further notice, so Bill and friends help Bev to remember the first time they met with their separate stories.
After hitting his head in a scooter accident, Waddle begins acting like a primitive duck and ends up on a billboard. Bill and Waddle then fall off of the billboard, and Raoul and his friends save the day.
Bill and Aldo find an egg in the park, with Bill thinking it's a duck egg and Aldo thinking it's an alligator egg. However, they are both proved wrong after it turns out to be a turtle egg.
Bill has to go out and buy a satellite dish in order to watch a special on The Flight Channel.
The cows have gone on strike, so the milk supply for the town is cut off. Bill is sent in to persuade them to start supplying again.
Fred likes Dottie and with Bill's help, nervously asks her out, but has to learn about using Bill’s scooter to get there. It turns out that penguins are not the best at scooter-driving.
After Aldo wins another bowling trophy, Bill realizes that he has never won a trophy himself, so he goes out to the city pond to fish for a rare marine animal.
After Bill hurts Raoul's foot in the window, he has to take care of him. However Raoul begins to take advantage of Bill even though his foot was never really injured
Bill decides he needs some time to himself only to find Ed, Waddle and Oly in his house watching TV. So he takes a boat to a private island only to have his boat float away. While on the island, he makes a new friend in a chicken and is almost eaten by alligators. When Ed, Oly, and Waddle notice Bill is missing, they set off to rescue him.
When Bill is almost eaten by a sleep-walking Aldo, he tries to get Aldo to eat duck food but to no avail. So Bill takes him to cecil which doesn't work and then tries a psychiatrist which also fails. In the end they find out that they both like to eat fish.
An alien named Zug visits Ducktown with a remote that can control people. Finding it funny at first, their opinion changes when Aldo is frozen, Ed, Oly and Waddle are put into a video game they are playing, and Bill gets shrunk. In the end Zug's parents arrive and he gets grounded.
To celebrate Penguin Day, Bill and his friends go down to central pond. However a fierce wind blows then over the to the alligators' side of the pond where they have to agree to play the alligators kids at a game of Ice Pucky or be eaten.
After Bill and Aldo have a fight over Aldo's clumsiness, Aldo leaves. Bill regrets the fight so Bill, Ed, Oly and Waddle head off to Swampwood to try and make up.
A boxing match between Crazy Bob the duck and an alligator known as the Green Death! has come to town and everyone is taking bets. However Bill finds out what is going on behind the match and then the tables turn.
After Aldo performs a magic trick on Bill turning him into a potato, Waddle babysits the potato he believes to be Bill for the day. In the end he realizes that he took the illusion a little too seriously.
Cecil shows Bill his new invention, ducky dentures, but says that the duck public isn't ready for the power of having teeth. Bill then takes the denture from Cecil's office and ends up having a dream that all the ducks have teeth and want to attack him.
Bill ask Aldo if he wants to go to a concert but Aldo refuses because he is too tired from work. When Bill asks what Aldo does for a job, Aldo refuses to tell him because his job involves cooking ducks. So Bill goes to Aldo's factory and is almost eaten by other alligators. Aldo finds Bill and claims that Bill is his lunch. In the end Aldo decides he is going to quit his job.
