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.
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.
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.
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.
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.
The Whiskers family gets separated when they go out foraging for the first time since they became a party of 40. The rival Lazuli tribe continues to cause problems.
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.
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.
Two young male meerkats are in charge of Meerkat Manor when Flower has a new litter of pups. Evicted Tosca attempts to rejoin Whiskers. While the Whiskers are out foraging, they come across a burrow belonging to their enemies, the Lazuli, with a litter of small pups.
Flower's new litter ventures outside for the first time to learn about the world they inhabit in the Kalahari, but since they are Flower's pups, just about all of the adults are on guard.
Evicted Tosca realizes she probably will not be allowed to return to Meerkat Manor, so she considers starting a group of her own. Flower leaves Shakespeare in charge when she leads the family on a search for food.
When the Whiskers family returns from foraging, they must fight off an attack by the Lazuli family rivals. The pups are safe, but Shakespeare has disappeared.