Ned is showing a health science project to his class that could make or break his passing grade, a film he's made to show where food comes from. The film is extremely strange, however, because of the various roles Newton plays in it: from the Hard-Boiled Chicken, source of the world's hard-boiled eggs, to the Imitation Crab, source of the world's imitation crab meat. Ned's project is initially doomed because of Newton's involvement, but Ned's teacher thinks that it was actually a creative writing project that was due the following week, for which he gets an A+. She wonders where his health science project is, and the final episode ends with Ned saying "I'll be right back," and leaving the classroom.

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Ned has been made the coxswain of the Friendly Falls rowing team in a regatta against the neighboring town of Carty Garbageton, a filthy town founded by janitors and gas station attendants. Friendly Falls traditionally beats Carty Garbageton, by coming in second-last. Their "winning" streak is in trouble, though, when Friendly Falls loses all its money sponsoring a start-up company to sell smoke and soot from the town's old chimney factory. Many of the townspeople have to do menial work in Carty Garbageton to make the money back, but they're all fired when the town starts becoming clean. Ned then gets the idea to sell the soot to Carty Garbageton, and the town makes all its money back just in time for Friendly Falls to not come in last at the regatta.

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It's time for the annual Friendly Falls Scavenger Hunt, which is mostly so that the town mayor doesn't have to do shopping once a year. Rusty McCabe is the favorite to win, but when Newton sees a rainbow, he thinks he'll find a pot of gold at the end. They do find the pot, but instead of gold, there's a universal remote that actually affects the universe, being able to pause time, make things go faster or slower, and so forth. Ned and Newton use it to thwart Rusty's victory, but each button only works once, so they need to get creative. They're about to win the scavenger hunt, when a group of leprechauns demand the remote back and hit the rewind button, rewinding the episode all the way back to the beginning.

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Ned has lost a tooth, and left it under his pillow for the Tooth Fairy. When the fairy comes, though, Newton thinks he's a burglar and attacks him. This results in the Tooth Fairy cursing Ned to have giant teeth, and Ned can only have the curse lifted if he does several tasks for the Fairy, such as counting all the newts in the world and doing his laundry.

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Ned's mother is hosting a Snapperware party, and Newton accidentally gets sealed in one of the containers and shipped away. Ned tries to find where the container has gone before it's too late.

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Ned is excited to be starting summer vacation, but is dismayed to find that July and August are missing out on the free gas station calendars everyone in town has, which leads the entire town to think that they're skipping Summer this year. Ned and Newton decide to investigate the missing months and find out that it's because the calendar publisher has lost the two artists that paint the banal scenes for July and August that go in the calendar. Ned and Newton have them quickly replaced, and Summer is saved.

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Ned gets a virtual pet toy, which makes Newton jealous. Soon, though, Newton finds out that the toy has artificial intelligence and intends to conquer the world. He tries to convince Ned that the toy is evil, but he doesn't believe him, assuming that he's gotten more jealous. It's up to Newton to defeat the evil virtual pet on his own.

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Ned has invited two girls, Linda Bliss, and a new girl, to the grand opening of the Friendly Falls Aquarium. Newton notices that Ned is anxious about this, and comes to the conclusion that it's because he's lonely. To help him out, he invites 310 more girls, to keep Ned company.

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Ned's parents lose all their money on a crooked insurance policy to insure several "valuable" things around their house, including a Gene Wilder bedroom mirror and a broken "unbreakable" vinyl record. This policy will only pay out if a series of impossible things damage these items, so Ned and Newton work together to destroy these items in impossible ways, get the money back, and thoroughly confuse the crooked saleswoman.

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Ned takes Linda to a sad romance film, Amour Amour Amour, and wants to take her to another one since the date was such a success. Newton gets an idea where he gets Ned's parents to dress as the film's characters while they go furniture shopping, and tells Ned that Amour Amour Amour 2 has been released the next day. Ned and Linda sit in a box that Newton pulls and drops to each floor of the department store his parents are at, and dubs over them to make it look like the film.

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Ned's parents are holding a costume party, but Newton had accidentally put the invitations in a wood chipper after Ned was supposed to mail them, so no one is coming. To make up for his mistake, Newton uses the time machine he built to gather several historical figures as party guests, including Cleopatra, Napoleon and Josephine, and Bonnie and Clyde.

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While on a field trip to the zoo, Ned and Newton decided to go to the bus through the emergency exit in the back. However, they find out that this door is actually a portal to a parallel universe, where the bus is parked in a lot of identical buses. They have to find the right one to get back home.

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After a freak accident, Ned and Newton switch bodies. They have to try to act like each other until they can switch back, but this is harder than it sounds.

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When Newton overhears Ned rehearsing his lines as a ring bearer at a family member's wedding, he mistakenly thinks Ned is going to marry someone other than Linda. He takes it upon his own to ruin the wedding, not knowing that it's not Ned who's getting married.

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While recording an episode of "Ninja Fish From the Outback", Ned accidentally records a secret message, after Newton does some "modifications" to Ned's television antenna. Ned's parents accidentally return the tape to the video store and are abducted and interrogated. Ned and Newton are sent on a mission of international espionage to recover the tape, find out its meaning, and rescue his parents.

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Ned signs up for the school debate team to be closer to Linda, even though he's bad at public speaking. Newton helps him by passing him notes, and Ned becomes the school debate champion. He's so good, in fact, that he successfully debates in favor of the town mayor's ridiculous plan to replace all of Friendly Fall's streets with canals, to ease pollution.

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While Ned's family is at the beach, a message in a bottle washes ashore, from Ned's long-lost Uncle Sandy. Ned and Newton decide to go rescue him, and get swallowed by a whale, encounter sirens, and get caught in a maelstrom before finding him. It turns out that he helped to invent the microchip, and as such, is a multi-billionaire.

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Ned's parents all go up to a cottage in the mountains, owned by Renfrew's parents, for some "peace". Renfrew's parents, unfortunately, are foley artists, and decide to catch up on some work while they're there. Things are made worse when Ned has to deal with Renfrew some more and gets lost in the woods while trying to re-enact the stories of fictional nature hero Woodsy Foreston.

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Rusty McCabe is well-known around town as a snobby rich boy, but when Ned's photos get mixed up with Rusty's at the photo booth, Ned finds out that Rusty's family is broke. At first, intending to disgrace him, Linda instead convinces him to be sympathetic, and people start donating things to Rusty's family. They later find out that these photos were from a theme park called "Live Like Ordinary People Land", where rich people pretend to be poor.

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Newton is worried that when Ned grows up, he will get rid of him. When he learns about the story of Peter Pan, however, he decides to take Ned to Neverland, where he won't grow up. Through a comedy of errors, however, Ned and Newton instead uncover an unlicensed video distribution operation.

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Ned has to do a local history project for school, but all of the good topics are taken. He soon finds out about the Friendly Triangle, an area in town where things allegedly disappear. He gets several eyewitness accounts of paranormal events in the Triangle, but when he tries to investigate them, he finds out all of his witnesses were just from a family with very poor eyesight that lost their things, and that the Friendly Triangle isn't real.

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Ned is excited to go to xylophone camp, but is dismayed to find out that no one there actually plays the xylophone, and that it's meant to be a camp for all the kids that couldn't get into "fun camps". After seeing that everyone is wasting their time on an electronic toy called the "Battery Drainer" because of its flashy commercial, Ned decides to create his own commercial to get the other kids interested in playing the xylophone.

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Ned sends in 20 cereal box tops to get a "Captain Ocelot Crypto-Claw" toy, but when it doesn't come for eight weeks, Newton decides to go and find it. After going through the company that makes it, they find out each of the toys is manufactured by a goat named "Inchina", and the box tops are meant to feed her as she makes each toy, which takes up to eight weeks.

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The carnival is in town, and Ned wants to take Linda to it. He's terrible at most of the carnival games, however, and Rusty McCabe beats him at all of them. Ned finds out later, though, that Rusty's uncle owns the carnival, and has rigged all the games to take the visitors' money and let Rusty win every time.

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Ned's class has started learning fractions, which Ned has difficulty with. To help him grasp the concept, Newton splits himself across the middle, but his lower half develops a mind of its own and tries to run away.

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Ned has started keeping a diary, but his entries are very typical and boring. To spice it up, Newton starts causing increasingly exciting things to happen in Ned's life so that he will have more to put in his diary.

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