Rocket Dog's pups, Nugget and Beaker, get their first lesson in Kalahari Desert survival as the Whiskers move burrows. Meanwhile, war breaks out over food and power at the Commandos, and Zorro teaches his brother Miles a lesson.
Sophie is back in the fold, and she and Axel babysit for Rocket Dog while the clan is away, but Sophie's attention is diverted by the arrival of Wilson and Axel is left to defend the burrow alone, which puts the pups in danger.
Rocket Dog needs a burrow where she give birth, but she can't find any; a pregnant Nikita of the Commandos chases away subordinates she thinks could harm her pups; Zorro finds out what life as a Commando is like.
Zorro, Rocket Dog's brother, leads a group of males in search of mates, and they hit the jackpot when they encounter the Commandos, leaving Zorro as their alpha male. Meanwhile, sister Sophie finds herself exiled.
Rocket Dog is pregnant and now has legitimate claim as the Whiskers' dominant female, but she still has a problem with sister Sophie, who may also be expecting and has injured herself while foraging for food.
Zaphod and six males leave the Whiskers for the Aztecs clan; Maybelline must keep her dad from chasing away the males, but one leaves to fraternize with a Whiskers female; Rocket Dog vies for his attention, but subordinate Sophie gets there first.
In the fourth-season opener, the original Whiskers clan splits into two groups, the Aztecs and the Whiskers, led by sisters Maybelline and Rocket Dog respectively, who both vie for supremacy in the Kalahari.