Season 3
01. Oh Brother
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02. Boo Boo Patrol
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03. The Legend of El Tomahto
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04. Interplanetary Kickle Ball
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05. Summer's Disaster-Piece
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06. Farewell, Statler and Waldorf
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07. The Mystery of the Missing Pearls
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08. Rowlf Gets the Blues
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09. The Copy Cub
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10. Animal Loses It
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11. Gonzo's Bubble Trouble
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12. Fozzie Can't Bear It
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13. Muppet Space Camp
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14. The Best Best Friend Beach Day
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15. The Ribbiter
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16. Presto Uh Oh
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17. Lone Eagle
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18. The Fellowship of the Rainbow Yo-Yo
Sam the eagle visits the playroom; Miss Nanny gives the Muppet Babies a super cool rainbow yo-yo, but only one person can play at a time.
19. Kermit and Fozzie's Eggcellent Adventure
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20. Animal and the Little Accident
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21. Backyard Safari
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22. The Invisible Frog
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23. Best Pals Pizza Delivery
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24. Summer Science Penguin
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25. A Very Sticker Situation
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26. Boo Boo Bamboozle
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27. It's Not Easy Being Greeny
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28. Dueling Harmonicas
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29. Best in Chicken Show
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30. No Takesies Backsies
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31. Sam and the Skyscraper
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32. Animal Too Loud
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33. Rozzie and the Big Bad Sound
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34. Muppets of the Caribbean
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35. Robin Digs Deep
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36. Fozzie and the Fairy Tea Party
Robin doesn't want to need his blankie every time he feels scared, so he asks Animal to hide it from him; Fozzie feels replaced when Rozzie wants to play with Summer and Piggy.
37. Gonzo-rella
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38. Summer's Car Trouble
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39. Rootin' Tootin' Sheriff Showdown
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40. The Trouble with Chickies
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41. Phantom of the Dollhouse
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42. Tarzanimal
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43. Scooter MVP
Scooter and the Muppet Babies come up with a plan to secretly let Skeeter win a sports game.
44. Rizzo for Mayor
The Muppet Babies hold an election for Mayor of the Playroom.
45. Kitchen Catastrophe
Chef is convinced Gonzo's cooking is yucky and refuses to try anything he makes.
46. Kermit Gets the Grumpies
Bunsen and Beaker remove Kermit's grumpies using their new invention.
47. Oh My Gourd
The pumpkin Kermit planted for Halloween is tiny.
48. The Curse of the Wereanimal
When Animal gobbles down too much candy without eating lunch first, he turns into the Wereanimal.
49. Moon Muffins
The gang bakes Moon Muffins, but Rizzo would rather relax than bake.
50. Muppet Newsflash
Piggy starts a news show, but the news in the backyard isn't exciting, so they exaggerate their stories.
51. Eagle in the Middle
It's scribble screen time and the gang can't agree on what to watch.
52. Rizzo's Space Race
Rizzo gets himself into trouble with Patch.
53. It’s a Wonderful Elf-bot
The Muppet Babies try to use Bunsen and Beaker’s newest invention, the Elf-Bot, to make Christmas gifts for Mr. Statler and Mr. Waldorf but they get so caught up in making gifts for themselves that they run out of supplies.
54. A Merry Litter Christmas
When one of Bunsen and Beaker’s new creations goes awry, they end up causing a huge mess on Planet Gonzo, so the Muppet Babies must come up with a plan to save Gonzonian Christmas.
55. Mitzvah for Miss Nanny
When Miss Nanny tells the Muppet Babies that she’s going to be doing mitzvahs for Hanukkah, they decide to do mitzvahs of their own.
56. Winter Sport-a-thon
Gonzo and Skeeter decide to hold a Winter-Sport-a-Thon.
57. Happy Villain-tine's Day
Gonzo turns into his alter-ego, Dr. Meanzo, when he thinks nobody made him a valentine.
58. My Best Toy's Wedding
Summer and Gonzo's best toys are getting married.
59. The Muppet Babies Show
The Muppet Babies feel excited to put on "The Muppet Babies Show" for all their friends before the playroom closes for summer vacation.