- “I'd be devastated if something happened to him.”
- ―Phineas Flynn
When Phineas and Ferb think Perry is lost, they use the power of music to find him. Meanwhile, Candace, who fears she is at fault for Perry's disappearance, combs the Tri-State area to find him. As it turns out, Doofenshmirtz has been downgraded to a low-level threat and Perry has been reassigned to a more dangerous villain, and a new family.
Phineas and Ferb are sleeping, Phineas holding Perry under his arm. Perry goes over to Ferb's bed, but receives a signal saying "Code Red" on his spy watch. When Ferb realizes that Perry is gone, Perry replaces himself with a log to reassure him. Perry then goes downstairs to enter his lair, but meets Candace on the way, who hasn't been able to sleep after eating a peach and pumpernickel sandwich. He reverts to his domestic house-pet disguise as Candace trips over him. She throws him outside, saying "For an animal that doesn't do much, you sure know how to make a mess of things!" Perry mocks Candace and enters his lair. Major Monogram tells Perry that he will be assigned to the Regurgitator, a new threat in the Quad-State Area, since Dr. Doofenshmirtz was downgraded to a minor threat. Major Monogram also tells Perry that he would also be assigned to a new family in the area as well.
Meanwhile, in the morning, Phineas and Ferb talk to Candace about Perry, telling her that he is gone. Candace begins to feel guilty but does not tell them that she put him outside. Perry watches Phineas mourning his loss through the window, then flies off. Perry flies past Dr. Doofenshmirtz's building. Dr. Doofenshmirtz, wearing a towel around his waist, reads a card attached to a gift basket, sent from The Agency to say that he has been downgraded to a minor threat. This hurts Dr. Doofenshmirtz, and he goes on his computer to research more about this "Regurgitator". Phineas and Ferb create a device to summon all of the platypuses in the Tri-State Area, so they will be able to find Perry. However, after they use it, they find out that there are many more platypuses then they thought. They try to figure out which one is Perry.
Dr. Doofenshmirtz tracks the Regurgitator to a broken-down motel, but it really a disguise for his lair. There, Dr. Doofenshmirtz realizes that the Regurgitator has already trapped Perry. The Regurgitator offers Dr. Doofenshmirtz a job as an intern, and he accepts. The Regurgitator tells Dr. Doofenshmirtz that he plans to destroy Perry. This angers Heinz, since Perry is his nemesis.
Meanwhile, the boys have checked through all the platypuses in the Tri-State Area, and none of them are Perry. Phineas then has a new idea, remembering how much Perry likes music. Candace, after failing her search for Perry, confesses to a shadowed Phineas and Ferb in a window that she was the one who put Perry outside the house at 3:38 A.M. When the lights come on, it reveals Marty the Rabbit Boy and his Musical Blender. Marty tries to cheer Candace up by playing Gitchee Gitchee Goo on his blender, but doesn't help. She then hears some music and goes to find out what's happening atop a building.
Perry helps Dr. Doofenshmirtz realize that he wants to be a main villain, not some intern. He tells the Regurgitator that he has had enough, listing all the things he's done. Unfortunately, he's installed an activated self-destruct sequencer and an escape switch inside Perry's trap. Perry escapes, and throws his water bowl to reverse the flow on the vacuum tube Doofenshmirtz entered by, causing the Regurgitator to be sucked through his lair's vacuum tube and fly all the way into the Agency's jail. Perry then escapes out of the lair, taking Dr. Doofenshmirtz with him. When Major Monogram tells Perry they have The Regurgitator in custody, they realize that they are both each other's nemesis again, causing Perry to drop Dr. Doofenshmirtz into a deserted plain.
Candace arrives at the top of the building to find Phineas, Ferb, Isabella, and the Fireside Girls, among their other friends, singing Come Home Perry. Perry arrives, and they all hug him, except Candace, who just smiles and says "Welcome home."
- Phineas and Ferb: A Very Perry Christmas
- Perry's supper bowl is a different color than in "Jerk De Soleil".
- In addition to proving beyond a shadow of a doubt that Perry loves his host family, this episode also proves that Agent P is a valuable agent in the Agency. His assignment as Doofenshmirtz's nemesis is changed because the O.W.C.A. doesn't need to waste Perry's talents on watching a mere "minor threat." It also suggests that Perry never arrests Doofenshmirtz so that he can stay with his family. ("Jailhouse Doof")
- This is the first time Phineas and Ferb worry about Perry when he goes missing because he left in the middle of the night. He's always home in the morning.
- At the end of Come Home Perry when Perry shows up, a group of kids come to hug the found Perry. But in the group, Isabella hugs Phineas instead of Perry, Baljeet appears to hugs Ferb, but his arm is shown to extend to Perry, he is hugged by Milly and Katie, who are dragged off by holding onto Baljeet. Holly and Ginger chase after them all.
- Jeremy plays the tambourine on the roof; he has no other involvement in the plot outside of this.
- During Come Home, Perry, all the clouds look like Perry.
- Linda was absent in this episode.
- One can see one of Perry's reaction towards Candace by imitating her behind her back.
- The Quad-State Area could be around four corners in Utah, Arizona, New Mexico, and Colorado, because of its desert-like appearance.
- When Doofenshmirtz is in the elevator to the Regurgitator's lair, The elevator music for I'm Lindana and I Wanna Have Fun! plays, though a bit faster.
- One of the rappers that sang S.I.M.P. (Squirrels In My Pants) can be seen in the crowd during Come Home Perry.
- Candace makes a chattering sound like Perry as she did when imitating Perry ("Does This Duckbill Make Me Look Fat?"). She is the first of three people, the others being Phineas and Ferb ("Interview With a Platypus"), to do so, and so far the only one to do it in more than one day. She also makes a face that is similar to Perry's when he is in "pet mode."
- The music in Come Home, Perry is similar to that used in A-G-L-E-T ("Tip of the Day").
- 'Momo' and the guy with the accent are briefly seen ("The Baljeatles", "Finding Mary McGuffin").
- Isabella doesn't speak, but is heard singing in the song ("Mom's Birthday").
- Balthazar appears during the song.
- Second time a flashback with younger Phineas is shown. ("Phineas and Ferb Get Busted!")
- The famous "Where's Perry?" and "Oh there you are Perry" are expanded in this episode.
- When Perry crashed into Candace, water got all over them. But when Candace put Perry out neither of them were wet.
- When Candace tripped over Perry, she lost one of her slippers, but when she tossed him outside, she was barefoot, having lost both slippers.
- Doofenshmirtz's BEST BOSS shirt had The Regurgitator's eyes brown, though they are really green.
- Doofenshmirtz said he installed an escape button in Perry's cage but it isn't shown in the trap.
- In the song, Phineas mentions that Perry is the color of a blueberry, yet in Does This Duckbill Make Me Look Fat?, Candace asks why her hand is green after switching brains with Perry.
- Right after Candace sings that she'll change her name to Larry, the crowd sings Larry one time. They sing it a second time when Phineas is shown, and Phineas's voice can be heard, but he's smiling, not singing.
- When Perry entered his lair Major Monogram said good morning even though it was late at night, although it could have been early morning as well.
- Ferb can be seen singing, but has no voice.
- During most of the episode when viewed on iTunes, if you look closely you can see a column on the left edge of the screen is lined out.
- Candace encounters Marty the Rabbit Boy and his musical blender in a store for the second time. He tries to cheer her up by playing Gitchee Gitchee Goo on his musical blender ("Flop Starz").
- When Dr. Doofenshmirtz finds a basket outside his door, he says, "Another Gift Basket?". He could be referring to the time when Perry brought him a gift basket for 'defecting to the good side'. ("Voyage to the Bottom of Buford")
- Lassie Come Home - The story is similar to Lassie's story. Also, the song "Come Home Perry" as a similar name of this story.
- Dora the Explorer - When Perry defeats the Regurgitator, Doofenshmirtz shouts, "We did it! We did it! ¡Lo hicimos! We did it!", which is an exact quote from the song "We Did It" in Dora the Explorer.
Pachelbel's Canon - The bass line of "Come Home Perry" is based on Johan Pachelbel's Canon and Gigue for 3 violins and basso continuo.
- Snoopy - There are two references in this episode that may be from this Peanuts film:
- Heavy Metal - The Regurgitator has a scary resemblance to Hanover Fiste from the "Captain Sternn" segment.
- SpongeBob SquarePants - The theme of the episode and the name of the song bear a very slight resemblance to the episode "Have You Seen This Snail?".
- The Beatles - The song takes place on a rooftop, much like the Beatles' last concert in 1969, even the guitar that Phineas uses is the same as the Epiphone Casino that John Lennon used in this concert. However none of the other instruments are the same.
- U2 - Where The Streets Have No Name - The rooftop concert is similar to the video by U2. The song styles are also musically similar.
- Frankie Valli - The melody of Come Home, Perry sounds very similar to the Four Seasons' 1962 hit Sherry (Can You Come Out Tonight?), especially the chorus.
- Vincent Martella as Phineas
- Ashley Tisdale as Candace
- Thomas Sangster as Ferb
- Alyson Stoner as Isabella (non-speaking role, singing only)
- Dan Povenmire as Dr. Heinz Doofenshmirtz
- Jeff "Swampy" Marsh as Major Monogram
- Dee Bradley Baker as Perry
- Mitchel Musso as Jeremy
- Bobby Gaylor as Buford
- Maulik Pancholy as Baljeet
- Clancy Brown as The Regurgitator
- Uncredited: Jennifer Stone as the Woman with a Pet Beaver
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