The first series introduces the Whiskers, a family of meerkats living on the edge of the Kalahari Desert. Shakespeare's life hangs in the balance when he is bitten by a puff adder, Tosca gives birth, and meerkat neighbours from another group cause problems. When Flower's daughter has pups, the Whiskers become a family of 37 and Flower must decide whether to keep all the pups or allow some to die so her own litter can survive. Youssarian decides to move the family from the burrow, a storm forces the Whiskers to take shelter in an empty burrow belonging to their archrivals, the Lazuli, and a terrifying battle ensues when the Lazuli return. The series ends with Daisy unexpectedly giving birth in the wrong burrow.
As series two unfolds, there is a sombre mood when Shakespeare fails to return. Meanwhile, the Whiskers take Flower's new pups on a foraging trip, new family the Commandos enter Whiskers territory, Flower decides it is time to move because the Whiskers have been at the same burrow for too long, and Mozart is forced to seek support from the Whiskers clan or risk losing the pups. Flower and the pups get into a fight with the Commandos, the Whiskers are forced to flee when they are caught raiding a burrow, heavy rains leave the Kalahari covered with lush foliage and winter returns as Mozart struggles to tend to her newborn pups alone.
As the series returns for a third run Flower leads the Whiskers to better hunting grounds, but the gang strays into the territory of the rival Zappa clan. Mozart and Kinkajou compete for the role of dominant female in the Starsky group, Carlos suffers from an infected wound, and trouble looms for the Whiskers when a group of Zappa males visit their burrow. Elsewhere, Punk takes charge of the Zappas and immediately begins planning an attack on the vulnerable Whiskers. Flower's daughter Rocket Dog takes charge of the Whiskers, Mozart and her sister Kinkajoo are forced to depend on one another for survival, Hannibal's son Wilson searches for some female company and sibling rivalry rears its ugly head as two sisters come to blows.
As the fourth series develops, Maybelline and Rocket Dog strive to regain control of their respective groups following Flower's death. Wilson makes a move to join the Aztecs group, Nikita defends her land when the Whiskers cross into Commando territory, Rocket Dog's pregnancy causes problems for her rival Sophie, and Zorro spots an opportunity to take over the Commandos. Rocket Dog searches for a new burrow in which to give birth, and her pups are put in danger when babysitters Sophie and Axel become distracted. Meanwhile, Maybelline and the Aztecs are forced to fight their way out of trouble, and Rocket Dog's pups receive their first lesson in desert survival. In the final instalment, disaster strikes at the Whiskers' burrow and the Commandos are on the warpath when Zorro disappears.