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.

The Kalahari is in serious drought, which splits the Whiskers for nearly a month. Although the Commandoes occupy the territory, Flower returns with half the group to their old manor in a desperate attempt to search for food. Flower's daughter, Rocket Dog, is left in charge of the remaining family and has problems dealing with leadership.

Big problems evolve at Meerkat Manor because Flower and Mozart are pregnant at the same time. Youssarian is left to babysit Flower's second litter of year. Mozart attempts to exert her authority on 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.

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.

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.

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.

Youssarian abandons his babysitting duties and leaves Flower's pups alone to face a terrifying rain storm. In an attempt to expand their territory, the rival Lazulis move a little too close to the Whiskers.

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.

The third season opens with Flower leading the Whiskers gang to better hunting grounds. When they cross into territory claimed by the rival Zappa clan, an altercation with them ends with a missing pup.

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

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, 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.

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.

The Commandoes, a new enemy family, spend the night on the Whiskers territory. A conflict ensues between the Whiskers, the Lazuli and the Commandoes.

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.

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.

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.

Flower decides it's time to move because the Whiskers have been at the same burrow for five weeks. She's in no mood for any nonsense due to her pregnancy, so her three daughters, Kinkajou, Daisy and Mozart, try to be careful or face eviction.

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.

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.