Flower gives birth to her third litter of the year. The Whiskers have reunited and have driven away the Zappas from their territory, then tragedy strikes the Whiskers family.

After Flower's pups go missing in Zappa territory, Mitch helps to reunite the family and the pups. During his mission, he encounters Mozart and Carlos, who have started their own group.

As Mozart's banishment continues, Flower and the pups get into a vicious fight with the Commandoes when the Whiskers get split up.

After being bitten by a puff adder, Shakespeare continues his struggle to survive. Carlos, a male from a rival family, threatens Flower's pups. The Whiskers have a territorial dispute with the Lazuli family. Daisy becomes overly friendly with Carlos.

In her final days of pregnancy, Rocket Dog seeks a new burrow so she may give birth to her pups. Zorro learns what being a Commando is like as Nikita exerts her authority on her pregnant subordinates.

When Wilson tries to join the Aztecs and Zaphod deters his encroachment, he seeks attention from one of the Whiskers females.

Maybelline dominance over the Aztecs begins to crumble and members start leaving the gang. Rocket Dog has similar problems with the Whiskers.

Flower's daughter has pups, making the Whiskers a family of 37. Flower must decide whether to keep all the pups or allow them to die so her own litter can survive. While searching for food, the wounded Shakespeare becomes separated from the group.

The Whiskers are getting acquainted with their new territory as Mozart and Kinkajou compete for the role of dominant female of the new Starsky group.

Winter returns to Meerkat Manor. The family has abandoned Mozart, who is trying to take care of her newborn pups. The rival Commandoes force a confrontation with the Whiskers.

Heavy rains leave the Kalahari covered with lush foliage, with tall grasses and beautiful flowers. Although life has never been better for the Whiskers, unusual conditions could mean disaster for the family.

Now that the Whiskers have split into two groups, the struggle for survival gets more intense. Daisy and Tosca begin a rivalry, but Flower solves the problem by evicting Tosca from Meerkat Manor.

Flower, as the dominant female of the group, has a lot to worry about, including her wounded son, Shakespeare, rivals, and her children's affiliation with the rivals.

Mozart is allowed to return to the family, but there serious consequences ensue when the Whiskers battle with the Commandoes. After three weeks of rain, Flower's newest litter of pups finally emerge from the burrow.

While on their first foraging trip, Flower's new pups are caught out in the open by a gang of war-dancing meerkats. Two of the Whiskers males who want to mate with Lazuli females join Youssarian.

Season 2 brings winter to Meerkat Manor. The Whiskers did not find Shakespeare after the Lazuli attack and he is presumed dead. Other tragedies are reshaping the families and Youssarian hopes to become the dominant male of the Lazuli clan.

As the Whiskers family is finally recovering from the split, more problems are created when Daisy gives birth to her pups in the wrong burrow and she needs help. Youssarian goes to her rescue.

Mozart, who was evicted from the Whiskers a month earlier, is pregnant. Without the family's support, her pups most likely will die. Flower has a new litter and the rain ensures there will be a plentiful supply of food for all the meerkats.

When the Whiskers are caught raiding their rival's burrow, they are forced to flee with dire consequences. Flower learns one of her daughters has a secret.

Sophie and Axel are distracted by Wilson when they are supposed to be babysitting, which leaves Rocket Dog's pups unattended. Meanwhile, Maybelline and Rocket Dog encounter difficulties of their own.

Lead by a pregnant Maybelline, the Aztecs battle former rivals while Nikita's pups create chaos in the Commando den.

Nugget and Beaker receive their first desert survival lessons. As the Whiskers move their burrow, the Commandos stage a war over rations and power. Meanwhile, Miles is taught an important lesson by his brother, Zorro.

Wilson and Phillippe leave on a mission to meet female meerkats and hopefully find a group in which they can join.

Rocket Dog's second litter of pups arrive at a time when the Whiskers are at their weakest. However, the survival of the new pups becomes uncertain when a dangerous situation presents itself.

Mitch becomes sick after he steals poisonous insects from his siblings. Mozart is given a reprieve and is allowed to return to Meerkat Manor after her eviction.

Sophie has problems with Rocket Dog's pregnancy, and the Aztecs find a new home with the help of Seacrest.

Survival takes center stage following Youssarian's decision to move the family from the burrow. To add to the problem, a thunderstorm threatens the family.

Mozart is evicted from the Whiskers family by Flower, and she is forced to leave her pups behind. Territorial drama ensues when the family takes shelter from the storm in one of the burrows formerly inhabited by the Lazuli family.

Although Flower's newest litter is welcome in the family, Mozart's unborn pups face an uncertain fate. She weighs her options as she tries to avoid losing her second litter of the year.

Carlos learns he has competition from Houdini from the Zappa group and the Starsky learn their new home may be temporary.

After Flower disappears mysteriously, Rocket Dog is left to lead the group. Dire consequences ensue when roving males from the Zappa appear and the pups become their victims.

Lola, the dominant female of the Zappa, is missing. In her absence, Punk attempts to take charge of the Zappa. When the wounded Lola makes her way home, she is greeted by a coup and her dominance is taken by her sister, Punk.