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.

As the season ends, the Whiskers now have 50 members. The new matriarch, Rocket Dog, attempts to maintain control of the group in spite of the efforts of her sister, Maybelline, to attain dominant female status. The group dynamic has changed and nothing will ever be the same again.

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.

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.

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.

Rocket Dog and her sister, Maybelline, compete as dominant female of the Whiskers. Zaphod exhibits resistance to the new leadership.

The Whisker pups are taken their first foraging trip to learn about Kalahari life. Mozart, Kinkajou, and De la Soul of the Starskys try to resolve a problem with an unfortunate resolution.

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.

A new roving male, Wilson from the Commandoes, joins the Whiskers and makes advances on one of the females. Mozart attracts the attention of a new male.

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

Led by Zorro, a group of Whiskers boys confront the Commandos, where the whole group stages a military coup. Meanwhile, Sophie is evicted from the Whiskers and could face living in exile.

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.

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.

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.

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

As the season changes, Zaphod leaves the Whiskers and begins a new life as a roving male. His attempt to find a new mate in the Zappa tribe is thwarted by the existing dominant male, so he decides to continue living alone.

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.

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.

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 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.

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.

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.

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.

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

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.