Ned goes with his dad on Take Your Child to Workday, and while he initially thinks his dad's job is dull, he eventually thinks that his dad is a government spy, and tries to find out more information.

When Ned complains that he can't go to summer camp, Newton mistakenly thinks he's describing boot camp. He signs Ned up for the army, and while no one notices that he's 10 years old and insists he does basic training, Newton tries to find a way to get him out.

Ned decides to climb a small hill to raise money for charity, but Newton thinks he would raise more if he climbed Mount Everest, so he takes Ned there and helps him climb it.

Winter is coming, and Newton learns that newts hibernate during the winter, a process he doesn't want to go through. When he learns that birds migrate instead, he decides to go away for the winter and takes Ned along.

Ned and his family are all set to spend a weekend in exciting Gamble City, but when Ned's mother finds out there's gambling there, she decides to have Ned stay with his aunt and uncle instead, who is a depressed, puritanical Eastern European couple who think fun is unhealthy. As Ned and Newton become more and more bored, Newton decides to have the whole house shipped to Gamble City.

Ned was born on New Year's Day, and as such, is expected to play Baby New Year every year at a New Year's Eve pageant. He doesn't want to do it at his age, so he desperately tries to find out if another New Year's Baby has been born in the town, saving him the embarrassment.

Ned's been given a small role in a horror film "Car-Driving Trees of Egstappa Part 2", but soon finds out that the Car-Driving Trees are real, and plan to wipe out Friendly Falls.

Friendly Falls is experiencing a drought, which is ruining Ned's summer, and might cause trouble for the various newts in town when the ponds and rivers they live in dry up. Newton tries to end the drought with various plans to make it rain, and they succeed, even though it has been raining so much the town flooded.

Ned and his friends are collecting 10,000 bags of pet hair for charity, but Ned's cousin Renfrew wants to sabotage their efforts. Newton will have none of it, so he attempts to get Renfrew off their case.

The Friendly Falls Future Fair has been reopened after it was closed in 1964, which makes Ned excited. The lineup to get into the fair is huge, though, so Newton sneaks him in so they can see the exhibits. Ned is dismayed to see that they haven't been updated since 1964, and most of the displays are ridiculous: there's a car with a record player mounted on the dashboard for a "car stereo system", a kitchen where malfunctioning robots cook food, and even robotic pets (much to Newton's shock). He goes back to his parents just as they get to the front of the line, and says he doesn't want to visit the Fair anymore.

Ned comes with his parents on their anniversary cruise, but thanks to Newton, he ends up on the wrong boat.

At Ned's family picnic, Newton develops amnesia, and thinks he is one of Ned's obnoxious uncles.

Ned visits his grandparents, who are retired farmers. Newton, who doesn't know what retirement is, thinks the animals and crops are simply being lazy and tries to whip them into shape.

Ned's mother goes to a different town to participate in a perfume saleswoman convention, but Ned mistakenly thinks that they are moving to this town. To convince Ned's parents that they shouldn't move there, Newton poses as a tour guide to describe various "horrors" throughout the town, and tries to make it seem as though wild boars roam the streets by putting boar masks on the stray dogs.

Ned's teacher has developed a new alphabetical desk arrangement, which unfortunately puts Ned in the back of the class, and Linda Bliss at the front. Because he wants to be able to sit right behind her, Ned and Newton arrange various schemes to make sure the few kids in between Ned and Linda get taken out of class, either by moving, being transferred, or having their last names changed. But at the end, when it looks like Ned and Linda get to sit with each other, Ned's teacher grabs him away from Linda and introduces to him two pairs of identical twins named Jenny, Kenny, Penny, and Lenny, who are told to sit between Ned and Linda, much to his disappointment.

Ned is made to play with his obnoxious rich cousin, Norman, who has a female pet newt. When Ned feeds both Newton and the other newt Zippo food, they both change, and Norman's newt wants revenge on Norman for constantly neglecting him. Newton falls for the female newt, whom he names Buttercup, and Norman is terrified by the two giant creatures that have suddenly appeared.

While Ned is working at a TV station, Newton accidentally destroys all of the station's pre-recorded content for the weekend, and he and Ned have to record all-new footage to replace it. They re-enact the news, several TV shows, and try to splice in whatever spare footage they can find to fill time.

When Ned's parents hear him talking about Newton, they assume this is a new imaginary friend, similar to one Ned had in his early childhood, a big talking red shoe named Shoe. They take Ned to see a child psychiatrist, but when they accidentally see Newton who has been going out and around in the form of a shoe since he found out about Shoe, and assume that Ned's imaginary friend is visible to them as well, they also go and see a psychiatrist. In the end, it turns out Shoe is real.

Ned notices that his alphabet soup is missing the letters N, E, and D. Curious as to why, he goes to the company that makes the soup, which turns out to be the same one that makes the Zippo Newt Food, to find out what's going on.

Ned has a cold, and Newton shrinks himself down so he can enter Ned's body and cure him.

With Mother's Day approaching, Newton thinks the purpose of the holiday is to give your mother as a gift. He finds his mother and proceeds to give her to Ned.

Ned's parents were planning a trip to New York City but had to cancel it when they heard, from Doogle's parents, that they've been watching a show about the urban legend that alligators live in the sewers. Ned and Newton go there to prove that the rumor is false, mainly trying to "blend in with the locals". But they end up falling into the sewers when they're ready to give up, and also accidentally find the sewer alligators.

Instead of a lemonade stand, Newton convinces Ned to instead start as a private detective service. Linda hires him to find her missing earring, and Doogle hires him to find his missing dog, Lummox. Ned eventually finds out that Lummox was accidentally made into a professional baseball pitcher, and then tries to find a way to get him out of the Major Leagues.

Ned had rescued an endangered plant for a science fair entry, but the plant soon starts to grow too much and threatens to take over the world.

Newton helps Ned and Linda win tickets to a rock concert, but their date is ruined when Doogle, while digging a hole to raise money for charity, accidentally unearths a race of subterranean trolls bent on taking over the world's "metropolises-es", and Ned and Newton have to stop them.