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.
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.
The Commandoes, a new enemy family, spend the night on the Whiskers territory. A conflict ensues between the Whiskers, the Lazuli and the Commandoes.
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.
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.
As Mozart's banishment continues, Flower and the pups get into a vicious fight with the Commandoes when the Whiskers get split up.
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.
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.
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.
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.
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.
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.