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.

פיניאס ופרב בונים כריש מתכת ענקי לרגל פסטיבל ימי הנמל, ובינתיים, קנדיס נחושה לכסח אותם.

פיניאס ופרב בודקים האם כוח הכבידה הנמוך שבירח יעזור להם ליצור את גלידה טובה.

פיניאס ופרב משתוקקים להעניק לאמא מתנה מרגשת. אז הם בונים מחשב כדי שיאמר להם מהי המתנה האידיאלית.

פיניאס ופרב בעזרת חבריהם, הופכים את בית המשפחה לבית-כיף.

קנדיס מאבדת את הטלפון הנייד ושוברת את המכשיר החלופי של אמה.

אבא נשטף בגל נוסטלגי כשהוא צופה בתכנית מילדותו, אך המסע של מרבד הקסמים הטלוויזיוני אינו מרגש.

קנדיס מסתפרת רע, ומבקשת מאחיה שיעזרו לה להיראות יפה לכבוד נשף הצדקה.

זהו פסטיבל הנקניק השנתי ואמא היא אחת השופטים שתקבע של מי הנקניק הטוב ביותר.

אמא מציעה לבלות את היום עם קנדיס והיא בטוחה שככה תוכל לכסח את האחים אבל הם משעממים!

קנדיס במיטה כשהבנים בונים מחולל יונים סטרטוספרי, וקנדיס רוצה בתשומת הלב של אמה.

המשפחה חוזרת מטיול ופיניאס ופרב מחליטים לבנות מסעדה על גג הרכב.

פיניאס ופרב מגלים שלבאלג'יט יש היסטוריה של הפסדים במרוצי אופניים, ובונים מסלול שיעזור לו לנצח.

קנדיס נרגשת כשהבנים בונים גרסת ענק למשחק השולחן האהוב "פקשושים".

קרובי משפחה של אבא מאנגליה מגיעים לביקור ובזמן שאבא ואחיו, מנסים להביס זה את זה במגוון תחרויות, פרב ופיניאס מוכיחים לקרוביהם את יכולותיהם בכדורגל ע"י בניית איצטדיון פוטבול.

בזמן שהבנים בונים משחק חיצים ענק, אמא עסוקה ביצירת אמנות מודרנית.

הילדים פוגשים את ראסל, בליל כל הקדושים שמספר להם שביתו רדוף רוחות.

פיניאס ופרב בונים המצאות שונות לבקשת חבריהם, אך כשקנדיס מוצאת אותן, היא משתכנעת שהיא ערפד.

בהשראת תאי המילוט מתקופת הוודביל, פיניאס ופרב בונים מגדל מחוכם ממנו יש להיחלץ.

פיניאס ופרב יוצרים בטעות אלפי תפוחי אדמה אנושיים.

פיניאס ופרב יוצרים שפה חדשה, שבמהרה הופכת לפופולארית בכל דאנוויל ודופנשמירץ מנצל את נורם כדי לגרום לכל התושבים לציית לו.

פיניאס ופרב מחליטים להתחיל את חג המולד בקיץ ומצלמים "ספיישל" לכבוד החג.

בתקופה פרה היסטורית, פיניאס ופרב ממציאים את הגלגל הראשון ואת המכונית הראשונה.

בסין של המאה ה-16, איזבלה הנסיכה נחטפת בידי דופוס חאן. פיניאס ופרב יוצאים לחלצה.

During medieval times, Phineas and Ferb (or, Ferb-a-lot) set off on an epic quest to find the legendary sword, Excaliferb, so they can defeat the evil sorcerer, Millifishmirtz.

פיניאס ופרב הם גיבורים בסגנון אינדיאנה ג'ונס שמחפשים אחר המקדש האבוד.

After losing a gift that Jeremy made for her, Candace is determined to recreate it before Jeremy realizes it’s missing. Unfortunately, Candace can’t remember what it looks like, so she enlists Phineas and Ferb to use their mind machine to enter into her subconscious and recapture the memory. Meanwhile, Doofenshmirtz’s evil plan is to use his Underwear-Inator to take over the Tri-State Area, since everyone's greatest fear is being caught in public in their underwear.

Thinking it would be cool to be part of an ant society, Phineas and Ferb create and infiltrate the Antius Maximus, a massive ant farm filled with giant ants. Suspecting that the boys are up to something, Candace accidentally drenches herself in the ant pheromones and follows them inside. Meanwhile, Doofenshmirtz feels tired and lethargic after eating turkey and decides to create a Turkey-Inator that will create a sleeping epidemic in Danville by turning things into giant irresistible turkeys.

פיניאס ופרב בונים את "גבינטופיה" - פארק שעשועים המבוסס על גבינה.

When Phineas and Ferb can’t find Perry, they decide to create the Perrytronic 3000, a mechanical structure that can assume any form. Of course, being aware of the boys’ every move, Candace decides to take a different tactic on her busting approach by using a new technique that keeps Phineas and Ferb from finishing their Perry project. Meanwhile, Doofenshmirtz invents a Duplicator-Inator-2 so that he can duplicate his own head and make himself twice as smart.

שוכרים את שירותיו של פרי לככב בקמפיין הפרסומי של "טוטאלי טולס" והבנים גאים בו.

פינאיס ופרב בונים מכונה נגד כוח הכבידה, שתאפשר לקפוץ על טרמפולינות.

Baljeet announces that he is no longer Buford's nerd, and Buford is heartbroken.

After Mom asks the kids to keep quiet while she prepares for her online knitting test, Phineas and Ferb create ninja outfits designed to hide the wearer from anyone who is not wearing them. Meanwhile, Candace becomes increasingly frustrated after she can’t find the boys and bust them. Across town, Dr. Doofenshmirtz invents the De-Handsome-Inator.

When Mom is out of Doonkleberries for her famous Doonkleberry pie, the boys set out to find some for her. Meanwhile, Perry and Dr. Doofenshmirtz find themselves across the ocean as Doofenshmirtz returns home to renew his Druesselsteinian driver’s license. Back in Danville, Candace is convinced she has discovered the answer to her busting problem.

Meap's world is put in danger and the boys try to help him save the universe when they travel to Seattle. Meanwhile, Doofenshmirtz visits former nemesis Peter the Panda.

פול, נער השליחויות מבקר אצל פיניאס ופרב ואז ממשיך לדופנשמירץ, שם רואה את המיצטרון.

Brigitte, Josette, and Colette, the visiting Fireside Girls from France, help Isabella capture the American Grizzly Bear, one of the world's most dangerous creatures. Buford's plan to jokingly dress up as the bear backfires when he discovers the identity of Brigitte, throwing him off his game. Back at their grandparents' cabin, Phineas and Ferb create the most amazing "run-through-the-sprinkler" experience. Meanwhile, Dr. Doofenshmirtz's loathing of pretzels drives him to create the "De-Twist-Inator" to untwist every pretzel in Danville.

When the boys ask Candace to decide what they should do for the day, she slyly asks them to invent a device to attract their Mom so that she can finally bust her brothers. Meanwhile, Dr. Doofenshmirtz has invented a "Baby-Cry-Inator" designed to tarnish his goodie-two-shoes brother's image with the electorate.

When Baljeet becomes concerned that he is losing his mental edge, the boys invent a cerebral stimulatory hat, or "Brain booster," to help him. But when the hat exceeds expectations and makes Baljeet exponentially smarter, he suddenly views everyone else as beneath him and becomes a threat to civilization by taking Earth's atmosphere and bringing it to the moon. Meanwhile, Dr. Doofenshmirtz plans to use his "Key-Find-Inator" to collect all the keys in Danville in hopes that it will lead to the Key to the City.

דופנשמירץ מתאכזב מכישלון התינוקטרון, ומחליט לזנוח את הרשע ולהפוך לטוב.

With Fall around the corner, Phineas and Ferb decide to invent "S'Fall", a colorful world full of giant leaf piles and gourds. Meanwhile, over at Evil Inc., Dr. Doofenshmirtz is mentoring Rodrigo, a budding student of evil. Unfortunately, Rodrigo truly is evil, and when he captures Dr. Doofenshmirtz and Agent P., it’s up to Major Monogram's son, Monty, to save the day.

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.

Candace's plans to hang out with Jeremy are derailed after he becomes interested in playing Phineas and Ferb's newest game, jet pack volleyball. Meanwhile, when Dr. Doofenshmirtz discovers he invents "-inators" in his sleep, he decides to go back into his dreams to find out what is happening.

Phineas and Ferb create their own flying saucer to help solve the mystery of a recent rash of crop circles. Meanwhile, Candace tries to give up her tattling habit by taking a "me" day, and across town, Dr. Doofenshmirtz challenges the local pizzeria's "37 Minutes or it's Free" rule by using his "dough-blow-inator" to generate a powerful current of air to hold the pizza dough aloft indefinitely.

Candace tries to bust Phineas and Ferb when they put on an enormous backyard magic show, while Vanessa and Major Monogram's son Monty get coffee together despite their warring fathers. Meanwhile, Dr. Doofenshmirtz tries to become hip in an attempt to get youthful followers.

The guys help their dad unearth a missing piece of Danville history; Doofenshmirtz tries to make himself younger to win a children's film festival.

Candace accidentally turns into a fluid when she comes into contact with a device that turns solids into liquids. Meanwhile, Doofenshmirtz turns himself into a platypus to defeat Perry in battle.

Candace finds it difficult to bust Phineas and Ferb when her brothers build nanobots that can assemble into any object they can imagine. Meanwhile, Dr. Doofenshmirtz has jury duty, so Norm takes over the day’s evil scheme -- to destroy Danville by using weapons.

The Flynn-Fletchers are off on an African safari, leaving Perry at home to deal with Doofenshmirtz and his most evil plot yet: to take over the O.W.C.A. But when Doofenshmirtz accidentally zaps Carl the intern with his Ultimate-Evil-Inator ray, Carl takes over the O.W.C.A. (Organization Without a Cool Acronym) and imprisons Doof and Monogram. Agent P steps in but gets zapped with Doof’s many rays and in the cliffhanger of all cliffhangers, disappears.

Agent P's fate is finally revealed in the action-packed finale of the two-part television special that left Phineas, Ferb and the gang hanging...literally off an unchartered gorge and Candace frantic over a phone call with Jeremy that left their relationship status in limbo. Now, with Agent P nowhere in sight, Dr. Doofenshmirtz and Major Monogram square off against evil Carl who controls a set of familiar-looking robots to take over the OWCA, in one of the biggest battles yet.

Phineas and Ferb create their own TV shows and commercials.

After discovering that a strange planet is hurtling directly towards Danville, Phineas and Ferb set out to avert a disaster, while Buford looks forward to making contact with its alien race. Meanwhile, Dr. Doofenshmirtz hopes to steal the world's largest ball of twine.

Phineas and the gang introduce Ferb and Perry to their newest project - training domesticated squirrels to live in the wild. Meanwhile, Dr. Doofenshmirtz aims to do a better job of seeing through his evil plans now that Agent P is back.

When one of Dr. Doofenshmirtz's "-inators" zaps him and Agent P into the middle of nowhere, they must embark on a comical journey filled with twists and turns to return home.

Agent P quickly figures out there is more to Norm's odd reality show that celebrates the eventful life of his creator Dr. Doofenshmirtz, which is recreated through flashbacks and special guests.

Candace is put in charge of Phineas and Ferb just before they seize the opportunity to make the most of Danville's electricity blackout while Dr. Doofenshmirtz tries to use pity to his advantage.