Mom leaves Phineas and Ferb a "huge list of chores" to do. In order to get the list completed faster, they decide to build teleporters to get around the house faster. Meanwhile, the evil scientist Dr. Doofenshmirtz, looking for a Peglegged Hemisphingus to complete his Official Tri-State Area Bird Watching Sticker Book, notices the teleporters and zaps one with a Duplicat-inator to copy it just as Phineas is going through it, inadvertently teleporting Phineas into his building. Ferb grabs a plunger and follows after his brother.
Meanwhile, the boys' pet platypus Perry is revealed to be a secret agent; he dons his secret identity and is given the assignment to stop Dr. Doofenshmirtz. As he kicks his way through a window and into the DEI building, Doofenshmirtz locks him inside a cage (which he is mass producing). He shows him the teleporters which he duplicated, which he calls the Transport-inators of Doom (pretending that he made them all by himself), which will allow how to produce more evil inventions, a scheme which he calls "Evil 2.0." Perry puts his hand in a teleporter; his hand then comes out of another teleporter and grabs the key near it to free himself. Seeing Perry escape, Doofenshmirtz escapes through a teleporter with Perry in pursuit. Perry is not able to catch him, and Doof returns to his lab. Angry that Perry escaped, he decides to activate his conveyor belts of doom, therefore giving Perry a harder time getting around the building, and hindering Ferb's attempts to reach Phineas as well. Perry makes his way to Dr. Doofenshmritz's lab, but Ferb makes no progress in his search.
Doofenshmirtz taunts Agent P that he's almost finished building 10,000 Transport-inators. Meanwhile, Phineas tries to look for a map but he presses a button at a computer terminal, activating the building's Freeze-inator freeze rays and setting off its intruder alert, causing Doofenshmirtz's security robots to capture Phineas and put him in a force field cage. Ferb successfully locates the three switches to reconstruct the bridge between Phineas's cage and the exit, disabling the cage and allowing he and his brother to successfully escape, although they do not see each other.
Meanwhile, Dr. Doofenshmirtz tries to freeze Agent P by firing a Freeze-inator at him (actually having a dentist appointment across town in half an hour, but staying "just for him"). Perry disables his two Transport-inator production lines, stopping any further production of the "Transport-inators" and then use a well-placed transport-inator to turn the Freeze-inator against Doofenshmirtz, freezing him and knocking him backwards into an infinite Transport-inator loop to defeat him and Evil 2.0.
Phineas and Ferb are reunited in their backyard, and Perry joins the boys shortly thereafter. Meanwhile, Dr. Doofenshmirtz is still stuck in the infinite loop, looking for someone to help him break it.
Ferb and Agent P control mostly the same with a few minor differences. The main difference is that Ferb can use his rocket boots to perform a double jump, while Agent P has a glider that allows him to glide. Along the way, each encounters a series of robotic enemies; cleaning robots require only one hit to defeat them, while security robots will charge when you get close to them and take two hits to defeat (in level 8, it takes three hits to defeat the large Hockey-inator robot). On each level, there are also anywhere from 100 to 400 gears or O.W.C.A. badges to collect, although it is not necessary to do so.
There are three types of power-ups in the game: a magnet that attracts nearby gears or badges towards you; a lightning bolt icon that turns Ferb or Agent P invincible and allows them to instantly defeat any enemies they touch; and a red stop sign, which stops all of the robots from moving for a limited time.
There are also several TV monitors that appear in both versions of each level. If you go near them, you will get a tip or a comment; to listen to it again, press enter in front of it. For Ferb, the people on the monitor are Isabella, Ginger, and Milly. For Perry, Major Monogram and Dr. Doofenshmirtz will appear.
The game features instrumental versions of a wide selection of songs from Season 1, most of which must be unlocked by finding the hidden CD in each of the game's 10 levels (including the tutorial).
- I'm Lindana and I Wanna Have Fun! or S'Winter for the holiday edition - title screen and menus
- One Good Scare - Level 10 (Bonus Music Player must be off)
- Today is Gonna Be a Great Day - during invincibility power-up
- Phinedroids and Ferbots - during stoppage power-up
- My Chariot
- Chains on Me
- Ready for the Bettys
- The Ballad of Badbeard
- He's a Bully
- Ain't Got Rhythm
- Backyard Beach
- Shooting Star Milkshake Bar
- Impress My Professor
- History of Rock
- My Goody Two-Shoes Brother
- My Nemesis
- Perry the Platypus Theme
- S.I.M.P. (Squirrels In My Pants)
- Gitchee Gitchee Goo
- Starting in late November 2010, the graphics of the game were given a special look for Christmas. Among the graphical additions include snow falling in the stages, Perry wearing a Santa Claus hat, and Ferb wearing reindeer antlers and a candy cane for a weapon. As of January 6, 2011, the holiday look disappeared, but is available by going to the setup menu and turning on "Holiday". The Holiday style was restored for December 2011.
- Several of the elements of this game are similar to that of the popular video game Portal.
- On level 9, it is possible for Ferb to jump onto the platform that Phineas is stuck on, though he does not acknowledge the fact that you are there.
- Doofenshmirtz steals another invention from Phineas and Ferb. ("Undercover Carl")
- Doofensmhirtz speaks whale again. ("Perry Lays an Egg")
- Doofenshmirtz says the following lines throughout the game:
- In the last cutscene, Phineas comments, "Pithy." ("Are You My Mummy?")
- Many pictures of different episodes are seen throughout the game.
- Young Heinz Doofenshmirtz and Balloony as well as Balloony floating away. ("The Chronicles of Meap")
- A picture of Perry tackling Doofenshmirtz. ("The Flying Fishmonger")
- A picture of Doofenshmirtz with the pigeons. ("Tree to Get Ready")
- A picture of Doofenshmirtz with the giant-robotic-icy-freeze-your-socks-off-breath-inator-thingies. ("Bowl-R-Ama Drama")
- A picture of Doofenshmirtz and some back-up dancers from "Impress my Professor". ("Oil on Candace")
- A picture of Doofenshmirtz looking evil and about to press the button of the De-Love-inator as well as a scene from Happy Evil Love Song. ("Chez Platypus")
- A picture Agent P and Doofenshmirtz eating popcorn. ("Greece Lightning")
- A picture of Doofenshmirtz seeing the white mouse running to charge his Deflate-inator. ("The Fast and the Phineas")
- A picture of Agent P and Doofenshmirtz having a tea party. ("Day of the Living Gelatin")
- Vincent Martella as Phineas
- Thomas Sangster as Ferb
- Alyson Stoner as Isabella
- Tiffany Espensen as Ginger
- Isabella Murad as Milly
- Dan Povenmire as Dr. Doofenshmirtz
- Dee Bradley Baker as Perry the Platypus
- Jeff "Swampy" Marsh as Major Monogram (uncredited)
- "Transport-Inators of Doom!" on the U.S. Disney XD website
- "Transport-Inators of Doom!" on the U.S. Disney Channel website
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