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.
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.
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.
Carlos learns he has competition from Houdini from the Zappa group and the Starsky learn their new home may be temporary.
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.
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.
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.
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.
Rocket Dog and her sister, Maybelline, compete as dominant female of the Whiskers. Zaphod exhibits resistance to the new leadership.
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.
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.
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.
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.