- A Muppet fanatic with some help from his 2 human compatriots must regroup the Muppet gang to stop an avaricious oil mogul from taking down one of their precious life-longing treasures.
- When 3 Muppet fans learn that Tex Richman wants to drill under the Muppet Theater for oil, Gary, Mary and Walter set out to find the Muppets who have been split up for years so that they can put on one last show and save the Muppet Theater. Kermit the Frog now lives in his own mansion depressed in Hollywood, 'The Great Gonzo' is a high class plumber at Gonzo's Royal Flush, Fozzie Bear performs with a tribute band called The Moopets, Miss Piggy is the plus-size fashion editor at Vogue Paris, and Animal is at a celebrity anger management rehab center in Santa Barbara.—Dre
- A middle-aged female and a middle-aged male and their male muppet friend do everything that they can to reunite the entire muppet group before it is too late. They all must perform to raise money to keep themselves in business and continue their careers.—RECB3
- Walter is a Muppet whose ambition is to visit the Muppet Theater in Hollywood. One day, he gets the opportunity to go, with his brother Gary and his girlfriend Mary. However, when they arrive they are saddened by the state that the theater has got into. When Walter discovers that oil magnate Tex Richman intends to buy the theater to drill for oil, he, Gary and Mary travel far and wide to reunite the disbanded Muppets. Together again, the Muppets must put on a show and try to keep their theater.—Anonymous
- Set twelve years after "The Muppets From Space". Walter, born a dwarfish yellow-skinned humanoid puppet, lives with his older brother Gary (Jason Segel), a human, in Smalltown. Growing as friends despite Walter being a social outcast, he two became Muppet fans when they watched "The Muppet Show" in their youths. As adults, Walter and Gary continue to live together in their home town of Smalltown. Gary plans a vacation to Los Angeles, California with his girlfriend Mary (Amy Adams) to celebrate their tenth dating anniversary, and he invites Walter along so he can see the Muppet Theater. Gary is pleased to spend time with both Mary and Walter ("Life's a Happy Song"), though Mary fears that Gary's devotion to Walter detracts from their relationship.
In Los Angeles, the three visit the Muppet Theater to find it in ruins. During the tour around the facility, Walter sneaks into Kermit the Frog's office and discovers Statler and Waldorf selling the theatre to Tex Richman (Chris Cooper), an oil-drilling magnate, and his associates Bobo the Bear and Uncle Deadly. Waldorf explains that the Muppets can raise 10 million dollars to re-buy the theater in a certain amount of days. Once Statler and Waldorf leave, Tex reveals himself to actually be a crime lord and Walter learns of Tex's true intentions: to destroy the Muppet Studios and drill underneath for oil.
Walter explains the situation to Gary and Mary, and the three track down Kermit at his mansion. Kermit is distressed to learn the news, and realises the only way to earn the ten million dollars would be to put on a show, which the Muppets have not done in years ("Pictures In My Head"), given the Muppets had disbanded after the events of the previous film. Walter convinces him to try anyway, and they set off to reunite the group. Fozzie Bear is performing with a group of uncouth Muppet impersonators, the "Moopets", in Reno, Nevada, and Kermit persuades him to leave the group. Gonzo has become a powerful plumbing magnate. He at first refuses, but secretly longs to return to his daredevil days; he then blows up his business and joins them. Animal is in a celebrity anger-management clinic; he rejoins them, but his sponsor, Jack Black, warns him to avoid drums. During a montage, the rest of the Muppets are found and picked up. They then travel to Paris, France to find Miss Piggy, who went to work as Vogue Paris' editor in chief. They try to ask her to come, but she refuses to cooperate. The Muppets replace Piggy with her Moopet counterpart, "Miss Poogy".
The Muppets pitch their idea for a telethon and are rejected by several TV networks. One executive, Veronica (Rashida Jones), accepts an offer to give the Muppets a 2-hour opening in her network's schedule, due to the sudden cancellation of one of the network's hit shows, however, on the condition that they bring in a celebrity guest. The Muppets repair the theater ("We Built This City"), but their rehearsal does not go well and Kermit is unable to find a celebrity guest. Miss Piggy returns and kicks Miss Poogy out. Kermit persuades Walter to help them out and find his talent.
Soon realising they have not found a guest host, Kermit asks Tex to give their studio back, but he refuses ("Let's Talk About Me"). Tex explains that he has had a grudge against the Muppets ever since they unintentionally ruined his tenth birthday party, and has since laughter in general because he had an inability to laugh. He further reveals that the Muppets will also lose their rights to the Muppet name; it will be given to the Moopets, who have allied with Tex. Miss Piggy then organises the Muppets, sans Kermit, to kidnap Black to serve as their celebrity host. Mary returns to Smalltown after Gary forgets the promised anniversary dinner. Gary and Walter each want the other's help with their problems, and they have a falling out. Gary realises that he needs to step up in his relationship with Mary, while Walter realises he was meant to be a Muppet ("Man or Muppet"). Gary returns to have dinner with Mary and they watch the telethon, which goes well with celebrity support and Black as host. Tex sabotages the power to the theater, but Gary and Mary rush back to Los Angeles and repair the wiring so the telethon can continue. Uncle Deadly turns on Tex and stops him from destroying the transmitter antenna.
With the telethon running short, Walter finds his talent by performing a whistling act to the audience's acclaim. The tote board stops at $9,999,999 after Tex destroys the nearby telephone pole and steals Kermit's car. A glitch discovered when Fozzie bangs his head on the tote board then reveals the total donations were actually only $99,999.99, nowhere near the amount of money needed. Kermit states that they tried and that is all that matters. Together again as a family, they will start over. When the Muppets, along with Walter, Gary, and Mary, walk out of the theater, they discover a massive crowd gathering of fans and press. With Gary's encouragement, Walter joins the Muppets as they greet the crowd ("Finale - Life's a Happy Song").
In an epilogue, Gary proposes to Mary, Black is taken and declared king of the hobos by Hobo Joe (Zack Galifianakis) and Friends, and Tex returns the theater and the Muppet name to the Muppets after Gonzo's failed "head-bowling" act from the telethon causes Tex a head injury, making him laugh for the first time in his life.
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