Farnsworth announces a "controversial" mission which involves towing a massive six thousand hulled tanker full of dark matter past protesters and Pluto where the penguins are. However, Leela refuses to participate, so Farnsworth strips her of command (and her leisure jacket) and gives command to Bender, who treats Fry like a work boy.
Leela joins the protesters, Penguins Unlimited, led by Free Waterfall Sr., who advocates that they form a peace circle around the tanker, unaware that the Planet Express ship can simply go over them. So the protesters prepare to move to Pluto to stop the delivery. Meanwhile, Fry gets fed up with Bender's obnoxiousness and ends their friendship. This drives Bender to not drink while captaining the ship, resulting in an upside down flight across Pluto. An iceberg gets through all 6000 hulls, dumping dark matter over Pluto and the penguins.
Bender is sentenced to help clean up the dark matter. But as the URL and Smitty are distracted by hugging, he disguises himself as a penguin to escape. His absence is noticed, so Fry and Zoidberg take the ship to find him, only to "leave" space and get attacked by a space squid. Bender, in the meantime, gets attacked by an orca whale. When he is found by penguins, his programming reboots to meet their specifications, making him think he's a penguin.
Penguins Unlimited finds that because of the dark matter, both male and female penguins lay six eggs every fifteen minutes. Because of this increasing population that will take out their food supply, Waterfall commences hunting season. Leela objects but Waterfall points out that overpopulation will make the penguins starve so she concedes. But when she finds a flock, she tearfully fires at one but it is actually Bender, who, when seeing Leela, reboots to his normal personality. He teaches the penguins to attack anything not black and white, killing Waterfall senior, at which his father swears to avenge him. Unfortunately, when Bender takes off his tuxedo, the penguins attack him and Leela, so they run to the sea and break off a raft of ice, only for the penguins to swim towards them. Luckily, Fry arrives, using the ship to tip the ice so the penguins fall into the mouth of an orca. As everyone returns to Earth, Leela hopes that nature will eventually correct itself. Unseen, two penguins pick up the discarded guns.