This is a list of episodes for the second season of Nickelodeon's animated television series, The Penguins of Madagascar, which began airing on March 13, 2010 and concluded on March 31, 2012.

After the penguins discover him in an underground bunker, legendary penguin agent Buck Rockgut drafts them to assist with apprehending the Red Squirrel, a top penguin enemy once brought down by Rockgut who has since escaped. Severely paranoid that they may be Red Squirrel agents, Rockgut begins to detain several zoo animals. Throughout, only Private believes such is wrong. He eventually tries using Fred as a Red Squirrel stand-in to trick Rockgut, but it backfires when Rockgut suspects Private of being the Red Squirrel himself. The other three penguins soon recognize Rockgut's errant paranoia and get him to leave by telling him the real Red Squirrel was in a made-up place called "Grrfurjiclestan". Later, a periscope is shown and it is shown that the Red Squirrel is real.

After creating a time machine called the "Chronotron," Kowalski is in need of one final chemical before he can fire it up for time travel. However, when he and the other penguins are out to obtain it, Kowalski's future self appears to Private and instructs him to not allow his present self to complete the Chronotron, lest great chaos in the future result. Later, as Private has no success in foiling the Chronotron, another future Kowalski appears to Skipper to ensure that his future self instead build the Chronotron. Eventually, the three Kowalskis see each other, creating a black hole in space-time. Two Kowalskis use the Chronotron to travel back in time, thus becoming those who had appeared to Skipper and Private. The space-time hole is then shut when Rico throws the Chronotron into it.

While the penguins are visiting with him in his sewer home, Roger, their alligator friend, states that he hates having to live there, but that he loves being in New York so much that he is willing to endure it. The penguins soon decide to help Roger find a better place to live in the city. They first hide Roger inside a log in a nearby pond, but a lady sees him and screams. They try hiding him as a display in a museum next, but Roger blows his cover by becoming "alive" when a boy pokes him. Following this, the penguins try to hide Roger on a rooftop as a gargoyle, but Roger, afraid of heights, soon falls into a public pool below. Throughout all this, the attempts to relocate Roger make TV news headlines, in a segment called "Gator Watch". While trying next to evade humans, Roger unwittingly enters onto a stage via a building's backdoor and is soon captured by animal control. The penguins then set off after the van transporting Roger to break him out, but they fail to do so before the vehicle arrives at its destination: a well-suited habitat at the Central Park Zoo.

In anticipation of the arrival of the zoo commissioner, a security detail quickly examines the zoo and its animals for threats. But as they leave, Skipper believes that the agents have done an inadequate job, so he and the other penguins take it upon themselves to ensure the zoo is safe for the commissioner's arrival to cut the ribbon on a new children's zoo. In doing so, they soon uncover that a pigeon, Frankie (Jeff Bennett), has plotted to "drop one" on the commissioner's suit in retaliation for his implementation of anti-pigeon park regulations. Skipper then tells the other penguins about how he had failed to act under similar circumstances when the previous commissioner had been attacked with bird droppings containing blueberries, vowing to not let the same happen again. The penguins then chase after Frankie, with Skipper flying through the air using a jet-pack, but the pigeon soon ends up releasing his blueberry-infused vendetta. Skipper dives in When Kowalski informs him that "The package has dropped" and takes the hit for the commissioner, and his team is horrified at the resulting look of their leader. Fortunately, however, Skipper reveals that he was wearing a "pigeon-proof vest" as he pulls it off his body. The vest is soon launched at Frankie via a makeshift cannon, resulting in the pigeon suffering the same fate he had intended for the commissioner.

When the penguins hear the scream of a child, they soon learn it was the result of a boy having been bitten by a sheep at the zoo's petting zoo. Appalled by the sheep's attack, the penguins set off at night to retaliate against him. However, the sheep, Randy, soon tells the penguins that he was provoked to bite the boy because the boy had, among other things, beaten on him and had pulled out a clump of his wool. Convinced that they had wrongly judged Randy, the penguins decide to help him out to prevent further abuse by rowdy children. When their attempts at applying a slippery polymer, building up static electricity on Randy's wool, and hypnosis fail, the penguins decide to transport Randy to a farm to live out the rest of his life. Randy is soon taken to a farm by the penguins in a truck, but shortly after his arrival, Randy is horrified at the appearance of the other sheep there, who are sheered and appear to be in a cult-like trance. Consequently, Randy ends up back at the petting zoo, but when the same boy approaches him to attack him again, Randy kicks him away. It is then revealed that Skipper and Rico had taught Randy some of their commando fighting moves.