It's been 10 years after the events of the present, and Phineas must decide what university to go to. After discovering that Isabella had a crush on him for years, Phineas must reach her before she leaves for college and express his true feelings for her. Meanwhile, Doofenshmirtz has a mid-life crisis.
Phineas and Ferb have created a device reinforcing the wind and test them on a giant kites in the park. Candace thinks she's finally going to bust when Mom gives her backyard a makeover. Meanwhile, Doofenshmirtz builds a Water-Zalewator to celebrate his girlfriend of the past, who doused him with water, because Heinz she loved, but who then gave him the basket.
Agent P travels to the glamorous city of Montevillebad to stop Doof from winning the Grand Prix and collecting the prize money. When Doof uses his "I-don't-care-Inator" to sabotage the race and eliminate the competition, including international racing legend of Italian-Scottish-Swiss-Dutch descent Paolo Vanderbeek (Patrick Dempsey), Agent P must take the wheel and go head-to-head with Doof on the racetrack.
Annoyed at waiting in really long lines at the return counter, Doofenshmirtz invents a "Back-to-the-Store-inator" to send things back to the store where they came. Meanwhile, Phineas and Ferb stage an extreme batting challenge their friends take place in, and Candace's obsession to bust coincides with her and Jeremy's visit to the Extreme Water Park.
When Candace is stumped about what to get Jeremy for his birthday, she reluctantly asks Phineas and Ferb for their help in creating the ultimate gift. Meanwhile, Doofenshmirtz plans to make fears a reality with his Worst-Fear-Inator, but his plans backfire when he finds himself battling his own fears instead.
After studying hours of horror movies, Doofenshmirtz develops a theory that enlarging small, cute animals into giant beasts will help him take over the Tri-State area. But when he puts his plan into action, he soon realizes it might be too much for him to handle. Meanwhile, Phineas and Ferb make a giant revolving foam city so they can safely perform skateboarding tricks, and Candace's tour of the Danville Space Laboratory gives her an opportunity for a high-tech bust.
After learning about Monty and Vanessa's secret relationship, Carl bribes Monty into helping him get some much needed acknowledgement from Monogram. Meanwhile, Candace is ecstatic when she discovers that her neighbor Peggy McGee has witnessed all of Phineas and Ferb's summer antics and is happy to tell Mom about them. Also, Dr. Doofenshmirtz creates its "Inflator-inator" to try to silence his neighbor who plays the bagpipes every day.
The boys set out to prove the existence of the elusive Chupacabra to the world, but Candace can't stand the wait and needs to first just prove it to Mom. Meanwhile, Doofenshmirtz has the brilliant idea to use his Switch-Place-Inator to remove hair from one person and give it to another so that he can in turn sell his hair growing tonic.
Dr. Doofenshmirtz and Major Monogram have their hearts set on revealing the top 10 musical numbers from Seasons 2 and 3, but soon find out that celebrity host Kelly Osbourne has been brought in to fill the role. Unwilling to submit to playing second fiddle, Doofenshmirtz makes it his mission to thwart Kelly until Perry the Platypus sets out to stop his nemesis from ruining the entire show. Maia Mitchell ("Teen Beach Movie") also guest stars.
When Pinky goes missing, Phineas & Ferb create a machine that will amplify Buford’s senses to those of a dog’s. However, it works so well that the animal agents’ secret identities are put in jeopardy. Meanwhile, Candace tries to meet up with Jeremy for lunch at City Hall but gets stuck in a mandatory tour.
When Candace thinks Jeremy is bored with their usual hangouts, she sets out to find something unique to do with him. Meanwhile, Phineas and Ferb power through town surfing on a giant ball of water and Doofenshmirtz plans to use his Double-Negative-Inator to confuse his local eatery into giving him a wintery drink that is usually not served during summer.
It's time for Danville's Doo Wop Hop and car show and the whole town is getting prepped for it. Doofenshmirtz is set on winning the show even if it means using his Rust-inator to turn all the other cars into red dust. Meanwhile, Candace's hope for a car of her own has come true, but it's not quite all she imagined.
Phineas and Ferb plan their own New Year's Eve ball drop, complete with a customized multi-dimensional ball, while Candace makes it her resolution to refrain from busting her brothers before the clock hits midnight. Meanwhile, Doofenshmirtz uses a Resolution-Changer-inator in his tie as he continues the never-ending attempts to take over the Tri-State Area.