The Pigeons of Madagascar is a parody of The Penguins of Madagascar (duh) using Animaniacs characters

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In a unknown place three young pigeons; The Godpigeon, Bobby and Pesto defy the laws of nature to save an cheeper the other pigeons believe to be doomed. After saving it from a pack of leopard and accidentally setting themselves in a ship, they meet the cheeper, Squit.

Some years later, the Godfeathers decide to leave Burbank to celebrate Squit's birthday by breaking into Fort Knox in order to treat him to a discontinued snack in the vending machine of their break room. Despite this, Squit begins to feel out of place with the team; as The godpigeon is the leader, Bobby is the strategist and Squit is the arsenal. Suddenly, they are abducted by the machine and sent to Venice, Italy by Doctor Octavius Brine a known scientist who removes his human disguise and reveals he is actually an orange dinossaur named Baloney, who has grown jealous of pigeons, after their nature of cuteness had shunned him out of the warner bos studios. Pesto stole his collection of snowglobes along with a canister of a green substance called the Medusa Serum before the four escape and are chased through the streets of Venice. When cornered, they are rescued by a group of animals from a spy agency called "The Girlfeathers", Three doves called Sasha, Lana and Kiki. Their mission; to protect the animals of the world who cannot protect themselves.

At their hideout, their communication systems are hacked by Balloney, who reveals that he has an enormous supply of the Medusa Serum and that he intends to capture the pigeons out of every city he was kicked out of. Not wanting the Goodfeathers help, Classified sends the group to their most remote base (which happens to be on Madagascar) but they awaken midflight and crash land in the Sahara Desert before making their way to Shanghai, which they mistake for Dublin, Ireland. Discovering Baloney's next target in Shanghai; the penguins ship themselves to their current location and go for it. Disguising himself as a pigeon to distract Baloney from his real target, Squit himself is captured along with the Shanghai penguins after the Girlfeathers arrives to put a stop to Balloney's plan. The pigeons take the Girlfeathers high-tech plane to give chase, but accidentally self-destruct the machine. They manage to track Squit to an island though, using a device planted on him when Sasha tranquilized them. Meanwhile, on the island, Balloney demonstrates his way to genetically mutate the pigeons into hideous monsters as an effort to make humans disgusted in them as revenge.

The Godpigeon and Sasha argue on the best means to rescue the captives and stop Balloney, settling on Sasha's plan of a frontal assault. They are quickly captured however, and the other pigeons are as well when the Girlfeaathers does not return. Balloney demonstrates his ray at full power on Squit, apparently disintegrating him with the beam, but unbeknownst to them he has escaped. Squit rescues the Girlfeathers who want to regroup but Squit, not wanting to leave anyone behind goes alone to stop Ballony. As Ballony's submarine docks at Burbank and he turns the ray on the rest of the pigeons, mutating them all into hideous monsters. The city erupts into chaos as the uncontrolled, mutated pigeons run amok on the terrified human crowd. Getting the senses back into the Godpigeon, Bobby and Pesto, they decide to connect the cute Squit into the machine to return them to normal. Balloney jumps into the path of the machine and is turned into a baby-like version of himself while the others attach his snowglobes to the machine, returning all the pigeons back to normal in one shot.

Squit is left mutated from the machine while the rest of the pigeons are restored to normal. Squit has been tinted pink and grown antlers. Despite his strange new look, the others show their gratitude and newfound respect for Squit. Balloney has also been made cute by the ray and stuck in a snow globe where he is found by a girl called Elmyra. Finally seeing one another as equals, the Girlfeathers promises to grant the Penguins anything they want. In addition to Bobby getting a kiss from Lana, the Goodfeathers are given their own jetpacks and then, they fly off above the clouds looking for their next adventure.

In a mid-credits scene, the Godfeathers return to Burbank and plug Dot Warner into the ray and use him to revert Squit back to normal, But she doesn't show any side effects from the ray, because she's too cute to be affected



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