After suffering incredible losses, the Penguin Defense Alliance regroups on RHC 23. Under the leadership of Lavour, Leepoh and Nok, the penguins implement a new strategy of survival. Foregoing the Overlord's ideas of conquest, they reform themselves as the Alliance of Independent Colonies and embark on a journey to the west coast of the South America to protect the threatened Humboldt Penguins. However, the Royal Emperor leadership has other ideas. The Overlord sends the vile General Diutes to RHC 23 to bring the alliance back under control and to educate those who fail to see their way. But the Rockhoppers of the island refuse to be intimidated and instead teach Diutes what it means to threaten a Rockhopper.
Plagued by the horrors of war and visions of his slaughtered colony, Lavour struggles to lead the new alliance. After nearly losing his life, the Chinstrap experiences a moment of clarity and realizes a truth too horrific to be believed. Aided by his friends, and with the hope of ending the conflict, Lavour leads the Alliance back to Antarctica to confront the Overlord and Supreme Commander Liutites.
Taking refuge in the ransacked GT compound, Gina and Randy ride out the dark Antarctic winter and with the hope of rescue and visions of a future together. But with each passing day the fear of being found by the Overlord's minions increases. When a powerful storm slams their sanctuary they find that it is not only the wind tearing at their defenses. With all hope lost, the pair finds that salvation can come in many forms.
The truth threatens to be revealed and both penguin and humans will stop at nothing to keep it hidden.