The film opens in springtime, about a year after Charlotte has died. Charlotte's three daughters, Nellie, Aranea, and Joy, are now in the stages of adolescence, with Wilbur serving as a companion and mentor.
During this time, Wilbur befriends Cardigan, a newborn lamb that is looked down upon by the other lambs and the younger sheep of his flock because he has black wool. Wilbur takes Cardigan under his wing and shows him the farm, the ways of animal life, and dangers to look out for.
However, after only a few weeks, Zuckerman suddenly sells Cardigan to another farmer, so Wilbur, along with Charlotte's daughters and Templeton the Rat, set out to visit Cardigan and make sure he is safe.
On the journey to visit Cardigan, however, Wilbur is hungry so he gets some grapes which make him look purple. Some bark from the trees comes and lands on his head. This makes him look like a wild pig. A near hit by a car then reveals that two other guys have now seen the wild pig. This makes it hard for Wilbur to visit Cardigan.
Meanwhile, an evil fox named Farley comes and steals a hen from the barn, and Wilbur is blamed. Farley comes and steals Cardigan from the barn, and plans to eat him. Wilbur now must save his friend, and does so by trapping him in a "pig web". Charlotte's daughters spin the word "fox" in a spider web, and Fern arrives just in time to save Wilbur. The fox, while not shown, is probably disposed of. Aranea and Joy decide to stay with Cardigan, and the film ends as Wilbur has to baby sit Templeton's kids. He had promised to do this earlier when Templeton had to get Wilbur out of some brambles bushes, which also helped make him look like a wild pig.
- Zecora, Stephen, Sharky, Mako, Willy, T.C., Hugs, Buzz, J.J., Socky, Skunky, 1206, The Miner Trains: (Steam Grindor, Steam Mech, Mucker, Steam Claw D., Steam Driller, Steam Sweeper, and Steam Exavator), Evan, Steamy, Puffy, Shai-Shay, Rattlesnake Jake, The Planet Trains: (Zip, Dazzlen, Dusten, Gustis, Rings, Uray, Tune, and Shiver), Dusty Crophopper, Bill and Ben, Rodney Copperbottom, Fender Pinwheeler, Wonderbot, Piper Pinwheeler, Crank Casey, Lug and Diesel guest star in this film.
- Nellie and Piper Pinwheeler are both voiced by Amanda Bynes.
- It's reveal that Steamy knows all about Farley.
- Web tryouts/The new enemy
- Arrival of Cardigan/"It's Not So Hard to be a Pig"
- At the fair/"Watch Out, Wilbur the Pig"/Cardigan sold
- Making a plan
- Setting off into the night
- Arrival at the Hirsh Farm/"It's Good to be Me"
- Farley strikes again/"Charlotte's Kids"
- Next morning/escaping the farm/The rescue!
- Saving Cardigan/Discovering the truth
- It's Not So Hard to be a Pig
- Watch Out, Wilbur the Pig
- It's Good to be Me
- Charlotte's Kids
- You're So True (end credits song)