To play a game of indoor hide-and-seek Phineas and Ferb shrink down their friends including, their new extreme fan, Irving. Meanwhile, Dr. Doofenshmirtz attaches a nanobot to Perry in an attempt to discover where he lives.

Phineas and Ferb discover the lost city of Atlantis, Candace enters a sand castle building contest, and Dr. Doofenshmirtz tries to use a growth formula to make plants evil.

Phineas and Ferb decide to help build floats for all the neighborhood kids in the yearly "Tri-State Area Unification Day" parade, but a family grudge leads Buford and his family to try and wreak havoc on the parade.

Irving’s brother Albert doesn’t believe that Phineas and Ferb are anything special, and since he claims to be the “Truth Detector,” he can prove it. Desperate to prove Albert wrong, Irving convinces Baljeet and Buford to pose as Phineas and Ferb beside a giant hologram of the boys’ Eiffel Tower construction. Meanwhile, Dr. Doofenshmirtz is fed up with the quality of accessories for his model train set, and decides to shrink down a variety of national monuments to add to his collection.

Phineas and Ferb head to the Tri-State area’s annual sci-fi/comic book convention to meet their hero, special effects guru Clive Addison. Their plan gets sidetracked when they’re swept into a duel between fantasy fans and sci-fi geeks. Meanwhile, Candace tries to keep secret that she’s a fan of Ducky Mo-Mo, another convention staple. Across the convention hall, Dr. Doofenshmirtz has taken television executive Jeff McGarland hostage so he can pitch him a show he’s developed, Doof ‘N’ Puss.

Phineas and Ferb plan to put Danville on the map by building the world's tallest building. However, Candace teams up with Albert and utilizes his expertise to bust her brothers. Meanwhile, Dr. Doofenshmirtz wants to be responsible for all the evil in the Tri-State Area, and since he believes that evil levels rise during a full moon, he plans to rotate it so that only the infamous "dark side of the moon" faces Earth.

It's Phineas' birthday and for the special occasion, Ferb puts together a clip show of the gang's favorite moments. Meanwhile, Agent P has to stop Dr. Doofenshmirtz from using his 'non-inator' to pre-empt his brother's biography from appearing on television.

Inspired by the lost verse from the nursery rhyme, "Hey, Diddle Diddle", the boys decide to take some cows to the moon to see if its low gravitational pull actually does produce the best tasting ice cream ever. Back at home, Candace decides to take advantage of the boys being gone and attempts to make a fancy dinner for Jeremy, but her lack of cooking skills don't add anything to the plate. Meanwhile, Dr. Doofenshmirtz attempts to use his 'Moisture Suck-inator' to turn his neighbor's plants brown, so that his plants will be greener by comparison.

Perry misses his 100th battle against Dr. Doofenshmirtz when Candace takes him to the Charity Pet Wash with her. Perry's absence goes unnoticed when the zookeeper's typical platypus at the Danville Zoo stops Dr. Doofenshmirtz's plan to zap his brother with his "Least Likely-inator." Meanwhile, the boys build a fun house Phineas and Ferb style.

When Ferb's cousins visit from England and challenge him to a soccer match, he and Phineas warp the walls of physics and build a high tech 3D stadium. Meanwhile, convinced that her relationship with Jeremy depends on her being more proper, Candace enlists the help of Ferb's British cousin, Eliza, to teach her the rules of etiquette. Back at Doofenshmirtz Evil Inc., Dr. Doofenshmirtz is sick in couch but forces himself to set off his \"If-A-Tree-Fell-in-the-Forest-Inator\", which causes any tree that falls to say his name.

Paul the Delivery Guy discovers his job has a higher calling to save Danville as he makes stops at Phineas and Ferb's house, Doofenshmirtz Evil, Inc., Danville City Hall and the OWCA, in a special episode seen through his eyes. The rock band, Love Händel, returns for some musical accompaniment. Meanwhile, at Doofenshmirtz Evil Inc., Perry has lost the tools in his hat.

When the boys learn that the famous Crikey the Crocodile has gone missing, they set out to find and return him to his home at the Danville Nature Preserve. Meanwhile, to Candace's amazement, Irving reveals his digital scrapbook compilation of all of Phineas and Ferb's wild creations, and guest star Ray Liotta fills in for Major Monogram to give Perry his mission. Also, Dr. Doofenshmirtz plans to embarrass his brother by using his 'Chicken-Replace-inator' to replace Roger's mayoral award with the nearest chicken.

The gang switches bodies with alien tourists for a free intergalactic vacation.

Doof's latest inator changes the way the Earth moves and it is up to Phineas and the gang to save summer.

Doofenshmirtz teaches an Inator Method seminar.

Doofenshmirtz's latest "inactor" turns Danville citizens into contagious zombies. Agent P. and the gang try to save the town and avoid becoming zombies themselves.

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.