The Animals settle into their new life in the promised land of Diamantina, but all is not well. Diamantina is plagued with earth tremors, one of which causes a rock slide that leaves Gertie trapped in a cave, and after Gorm confesses that Diamantina floods during the night of a full moon, the other animals begin to blame Noah for leading them to a place where they're always in danger. Elsewhere, Chang discovers a cave full of beautiful jewels, but when Ursula finds out about the cave they argue over ownership of the jewels.

The Animals stop listening to Noah and turn against him in the aftermath of the flood. Meanwhile, Diamantina's other residents, a race of prehistoric frogs, learn of the inhabitants of the floating Island, and seeing them as invaders, they prepare to fight back...

Noah and Gertie decide to set off on the floating island to find mates for the other animals so their community can grow. For their first mission, they travel to Africa to find a mate for Reg, bringing back a boisterous female baboon named Rita. Gorm is outraged by Noah and Gertie's plan, believing that more animals coming to Diamantina will ruin his peace and tranquility. Queen Abront advises Gorm to kill the "Invaders", starting with Reg.

Gertie gives Sacha the job of Diamantina's "Newshound", in which he has to travel around the community and report current and upcoming events, but he ends up spreading gossip and secrets that he overhears. Meanwhile, Noah, Gertie and Wommie go to Australia to find a mate for Woomera, and Reg steals all of Diamantina's bananas to impress Rita, causing upset among the community's primates and further angering Queen Abront and the frogs.

Wommie the Wombat is appointed as Diamantina's law enforcement, but he abuses his newly gained authority by arresting animals for the smallest of offences, such as Mammothsbody sucking his trunk and Carmen eating ants without a "licence". Meanwhile, Chang and Ursula find a strange man-made machine washed up on the beach, and upon discovering it has a camera and human voices coming out of it, Noah orders to have the machine destroyed, believing that it will lead humans to Diamantina.

Salomi senses that Diamantina will flood again, so Noah orders Sacha to spread the word of the next flood. Rocco and Gertie plan to build a rock wall in front of their cave's entrance to protect the animals from the flood, while Noah and Nab struggle to find enough lava stones to fuel the Fire-Bowl. When Noah finds out what Rocco is planning he sets out to stop the wall from being built and convince Rocco that the wall won't protect them.

Noah and Gertie go back to Africa to find a mate for the Valve Rhino, but because the Rhino has charged off into the forest, they ask Gorm to push the valve system in the Fire-Bowl. The Rhino wanders into Queen Abront's cave, and Rocco and Woomera venture in to find him, but get lost in the tunnels. Meanwhile, Galleo eats the lice Sacha was collecting for his insect circus, so Sacha believes that a monster is on the loose and sets out to find more lice.

An enormous iceberg floats by the coast of Diamantina. The animals who are more used to colder climates, such as Noah and the Problem Walrus, are delighted by the sudden cold snap the iceberg brings, but everyone else tries to escape the cold by sleeping in the Fire-Bowl chamber. Upon discovering that there is a deep crevice within the iceberg, Gorm and the frogs devise a plan to trap the animals inside, so when the iceberg leaves it will take them with it.

Gertie takes up the hobby of weaving raffia. Rocco is initially annoyed by the large amounts of raffia in his cave, but upon noticing the substance's strength, he comes up with the idea to construct a chair-lift that goes across Diamantina using the raffia as a cable line. Most of the animals are supportive of the idea and help Rocco set up the raffia cable, but Gorm is once again angered that the animals are ruining his paradise. When Reg and Rita tell Queen Abront what is happening, she sends Reg to sabotage the construction of the chair-lift.

Boredom sets in to the residents of Diamantina. The frogs and Reg set off to find the very rare Diamantina Rose, which only grows once every 100 years. Sacha meets the frog he saved a while back, and is asked to teach the frog some circus tricks.

The animals take pieces from Diamantina's coral reef to help Gertie decorate her cave, but the removal of coral from the reef has unexpected repercussions. Noah joins Sacha's newshound team to head spread news faster.

Earthquakes are becoming more frequent in Diamantina. Gertie realises that Diamantina is not a safe place to raise her unborn baby, so despite Noah's protests, the Animals prepare to leave Diamantina for good. Ursula is elected as a new captain.

The animals still aren't convinced after Noah's attempts to persuade them. The animals board the island without Noah. Meanwhile, Reg and Sacha are requested to help the Queen Frog.