The third season begins with Phineas and Ferb building a gigantic biome during a bit of bad weather to help Isabella earn a Fireside Girl patch.

Candace realizes that she needs to spend more time with Stacy, so she vows to spend the whole day with her only. But while visiting Jeremy and his mom, Mrs. Johnson, Dr. Doofenshmirtz's "combine-inator" zaps her and Jeremy, literally joining them at the hip. Meanwhile, Phineas and Ferb build a giant robot dog that causes a lot of mischief.

Phineas and Ferb's newest invention is a pair of boots that make the wearer extraordinarily fast. Candace decides to wear them so that she can be in two places at once; at Jeremy's family picnic, where she runs into Mrs. Johnson, and also at the library where she promised Mom she would read to the kids. Meanwhile, Dr. Doofenshmirtz's building is put up for sale so he tries to convince a prospective buyer, Annabelle, who turns out to be a long lost relative of the Johnson family, that it is not worth buying.

While visiting their grandparents, the kids decide to create and race a giant hot air balloon. Meanwhile, Candace is inspired by train engineer Glenda's can-do attitude and decides to "give up" on busting her brothers. On the other side of town, Dr. Doofenshmirtz finds a Dodo bird egg and is convinced that it is a fierce bird-monster that can help him take over the Tri-state area, but discovers the exact opposite when the egg hatches.

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.

For Harbor Days Festival, Phineas and Ferb celebrate by creating a mechanical version of the historical elusive shark of Danville Harbor. Seeing what the boys are up to, Candace enlists some help to capture the mysterious shark. Meanwhile, Dr. Doofenshmirtz invents the 'Salt Water Taffy-inator' to give cavities to every kid in the Tri-State Area.

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.

When Candace discovers that Phineas and Ferb have invented a computer that can answer anything, she asks it how she can finally bust her brothers once and for all. Meanwhile, Dr. Doofenshmirtz loses the key to his latest invention, the "All Purpose-inator," and Agent P must find it before he does.

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.

Candace has no choice but to go to her brothers for help after she loses her phone for the fifth time. Unbeknownst to her, the phone that they invent for her has a voice activated phone transfer app that sends her to Easter Island. Meanwhile, back at Evil Inc., Dr. Doofenshmirtz invents a "Pick 'Em Up-inator" to pick Vanessa up from class, then he finds Sarcastic Norm Head, the Norm head prototype that has an affinity for sarcasm, later Doofenshmirtz and Perry watch an exercise show.

Inspired by Dad's favorite childhood program, the boys decide to create a magic carpet, and Candace is convinced that fortune cookies will lead her to bust her brothers. Meanwhile, Dr. Doofenshmirtz plans on ruining his brother's art unveiling by using his "Stain-inator" to ruin a mysterious painting, but as it turns out, the painting is Dr. Doofenshmirtz's very own masterpiece that he created when he was a youth back in Gimmelshtump.

Candace gets a bad haircut and must rely on Phineas and Ferb's hair growing machine to correct it before she attends the Endangered Animal Benefit with Jeremy and his mom. However, when Candace turns up the power, her hair grows much more than expected and she is mistaken for a rare tangerine orangutan. Meanwhile, Dr. Doofenshmirtz is developing his Very, Very 'Bad-inator.'

Mom joins Jamie Oliver as one of the judges for Danville's Meatloaf Festival Cook-off, as he stresses healthy eating and fresh ingredients. Meanwhile, Candace puts a bid on a prized souvenir resembling band members Nigel and Adrian from her favorite band, Tiny Cowboy, at the Rock and Roll Memorabilia Auction, but gets distracted when her brothers build a bounce house in their backyard. On the other side of town, Dr. Doofenshmirtz has plans to enter his family meatloaf recipe into the competition using "hate" as the special ingredient.

When Mom tells Candace she wants to spend the day with her, Candace spends the entire time with her in the backyard so that she can bust her brothers. Unfortunately, Phineas and Ferb's grand plan for the day only entail watching the grass grow after getting zapped by Dr. Doofenshmirtz's Dull-and-Boring-inator earlier that day. Meanwhile, Agent P partners up with Dr. Doofenshmirtz to fix the now destroyed Dull-and-Boring-inator into a Dynamic-inator in order to fix Phineas and Ferb.

When Dr. Doofenshmirtz thinks Vanessa overhears him say he would rather have a son to do his evil bidding, he feels terrible so he intends to zap her with the "Forget-about-it-Inator." Meanwhile, Norm shares his feelings of wanting to be a real boy with Dr. Doofenshmirtz and decides to play up the "son" role. Back at the Flynn-Fletcher household, Candace has Stacy hypnotize her into ignoring the need to bust her brothers so that she can spend the entire afternoon relaxing with Jeremy, but unfortunately the hypnosis trigger words end up playing right into her date with Jeremy.

After Candace injures her ankle and is told to stay in bed, she drives herself crazy trying to get her Mom's attention in order to bust her brothers. Fortunately, Phineas and Ferb provide her with a box of items to stave off her boredom. However, it ends up being more of a hindrance, until she unknowingly helps the boys warn their cosmonaut friend about a dangerous obstacle approaching them. Meanwhile, Perry interrupts Dr. Doofenshmirtz's Chicken Soup themed escapade.

On the last day of the Flynn-Fletcher family road trip, Candace thinks she’ll finally have a couple of hours to relax and not worry about busting her brothers. However, Phineas and Ferb decide to build a truck stop diner on top of the RV. Meanwhile, Doofenshmirtz is also doing a road trip, but he’s using a big rig to transport his boom juice across the Tri-State Area.

Phineas and Ferb enlist the help of cyclist Greg LeMond to help Baljeet compete in a bicycle race. Meanwhile, Doofenshmirtz tries to bring the city to a standstill so he can bid on an auction unopposed.

Phineas and Ferb build a giant version of a favorite childhood game, with Danville as the central location. Meanwhile, Doofenshmirtz takes Vanessa on a camping trip.

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.

When Lawrence heads out to attend a speaking engagement on antiques, he unwittingly finds himself participating in the L.O.V.E.M.U.F.F.I.N. Pageant of Evil against Dr. Doofenshmirtz and Rodney. As a special host oversees the proceedings, Perry is tasked with monitoring the situation, but Lawrence gets hit with Rodney's "Make-Everything-Evil-Izer", and is crowned the supreme leader of L.O.V.E.M.U.F.F.I.N. Meanwhile, Candace is determined to bust the boys but doesn't realize that the object she's looking at is not theirs. Across town, the boys are playing a giant game of darts.

It's Halloween night and the kids encounter a strange boy named Russell who is convinced his house is haunted. Meanwhile, Dr. Doofenshmirtz's disdain for grass causes him to invent a "mind-transfer-inator" enabling him to merge minds with a cow and destroy all the grass in the Tri-State Area. Unfortunately, his plan backfires and he transforms into a scary "were-cow" that wreaks havoc any time there is a full moon. It's now up to Agent P to stop him and save Danville.

Candace is bitten by a bat after watching a popular vampire movie with Stacy and worries that she is becoming a vampire. Phineas and Ferb's latest gadgets lead Candace to believe that she has indeed made the change from teenager to teen vampire. Meanwhile, Dr. Doofenshmirtz plans to change the Tri-State Area into a carbon copy of Gimmelshtump so that it will be easier to take over.

When Phineas and Ferb are inspired by an antique escape chamber that Dad acquires, they decide to build a computer-controlled tower that will trap them inside and allow them to explore the world of escapement. Meanwhile, Dr. Doofenshmirtz invents a "Rude-Inator" to ruin Roger's meeting with a visiting dignitary from England.

Potato gremlins appear all over town when Phineas and Ferb clone a potato chip from Buford and it mixes with his DNA; Doofenshmirtz tries to summon the Spartan army with his historical army retrieve-inator.