Season 2

Coming away from the Antarctic Coast, the Island is getting closer to Diamantina, but Salomi is worried that she will die when they reach the paradise, which frightens Mammothsbody. Meanwhile, a cargo plane crashes on a nearby reef, and Noah and The Problem Walrus swim out to investigate. They rescue Gertie, a female gorilla who was born and raised in a zoo, and bring her back to the island, but Gertie's loud and bossy personality soon begins to annoy the other animals.

Noah's Island has come alongside the great continent of Australia and Woomera is feeling homesick. Tired of being bossed around by 'a blinking gorilla' named Gurtie, who is orchestrating a mass replanting of the island from an Australian oasis, Woomera decides to check out her old stomping ground and heads off into the outback. After being challenged by Gurtie that bandicoots have now become extinct, Woomera sets off on a mission to find one but instead meets a wombat (Wommie). Wommie informs Woomera that the bandicoots have all been eaten by the Bunyip yet she is undeterred by this and is insistent on finding one. Meanwhile back on the island Jasper has spotted a tornado heading directly for them; it is then Noah's task to bring Woomera back to safety and so the island can resume its journey. Woomera is successful in finding her bandicoot and the gang leave Australia in one piece.

An approaching tidal wave threatens the Island, so Noah sends the Vulture Patrol to search for another island that they can hide behind until the wave passes. The vultures succeed in finding a suitable island, only to discover that it is populated by hundreds of green parrots that refuse to heed their warning of the impending tidal wave.

Rocco is very proud on the day in question as his first 'silver hair' has appeared on his back. Being a Silver Back Gorilla it is a momentous occasion for him. Meanwhile Reg has become sucked into a whirlpool that has appeared on another end of the island. Reg is fascinated by his discovery of a giant clam containing a huge pearl at the bottom of this watery apparition. The rest of the animals attempt to save him but all inevitably fall in as well. With a little assistance from Noah and Salomi, the stranded animals are rescued. However, Mammothsbody, on the escape from the whirlpool's depths, strangely pulls out and eats Rocco's silver hair.

Wombat (Wommie), a new member of the island has made a didgeridoo and its strange sound is attracting butterflies from everywhere. When Reg discovers this strange instrument's talent he relieves Wombat of it and takes up butterfly collecting. He soon discovers that Noah's Island is about to pass an uninhabited island which is likely to be a great chance to hunt down some new specimens to add to his collection. After tricking Rhino into adjusting the firebowl valve, Reg swims ashore, with Sacha and Noah in hot pursuit of him. The trio shortly discover that the only indigenous life on this island is a formidable, meat eating plant that seems to cover most of the island floor. Sacha is the first to fall victim to these evil plants' dinner plate but Noah comes swiftly to the rescue, swinging from the trees above in a Tarzan re-enactment to rescue his little friend. The other animals soon realise that the three are missing and turn back to the island and rescue them.

Whilst Reg is mucking around on the beach, an old foe of Mammothsbody's surfaces: the shark. Squadron leader saves Reg from the wrath of this vicious marine creature but is fatally wounded and is convinced his time is up. With the Squadron Leader's impending death he decides that a competition must be held to determine who will succeed him as leader of the vulture patrol. A variety of contests take place including "Whelk Slurping" and "Pin the Tail on the Wildebeast", who is actually Mammothsbody (who is terrified that the vultures will "eat" him). Even though Reg is appointed as chief judge, many of the vultures end up in the infirmary. Then through a strange course of events 'Baby Chick Bird' wins and becomes designated the new squadron leader. After a brief speech at his inauguration ceremony the weak, old 'Squadron Leader' realises he still has "much to teach" his vulture patrol and conveniently rearranges his appointment with the Grim Reaper.

A heat wave passes over the Island and the animals all try to keep cool. Noah and Wommie rescue a pangolin who is adrift on a log and bring him back to the Island, where he immediately befriends Carmen the Aardvark. After Carmen and the pangolin eat the queen of a termite colony, Sacha offers himself as a replacement queen, but the termites capture him and imprison him in their nest. Upon hearing what has happened, Noah sets out to try and rescue Sacha. Meanwhile, the strong heat causes Woomera to faint, and Rocco fears that she may die of heat stroke...

The Island has some univited visitors in this episode. Snakes arrive to wreak havoc by biting nearly every animal they meet. With the casualties mounting Noah looks to the vulture patrol to bring a mongoose from the mainland to help them. The vultures come up trumps and locate such a mongoose who then treats the bitten with his herbal medicines. Noah however gets spat at by the snake ring leader (a cobra) and is blinded. Luckily for him the effects are only temporary and his sight returns. The snakes are forced into retreat. Meanwhile Mammothbody fights the shark using problem walrus as a club. the snakes are loosed onto the sharks tail leaving island for good.

The Island floats through oil-polluted waters, and as the beach becomes covered in oil, Noah is stuck with what to do. Goosey and Salomi suggest that they find a golden mole, a rare animal that is rumoured to have magical powers and never fail in navigation, and Noah, Sparky and Sacha travel ashore to the Arabian desert to find a golden mole.

The Vulture Patrol returns from a scouting mission on the east African coast and tell Noah that they saw some animals trapped in a long-abandoned zoo. Rocco and Ursula are sent out to help the animals, and Rocco recognises the zoo as the one he was born and raised in. During the rescue mission, Rocco is reunited with Imshee, a warthog he knew when he was a child. Meanwhile, a stampeding herd of gnus find their way onto the Island and wreak havoc.

The Island travels past Madagascar, and Ursula decides to do a good deed to redeem herself for past mistakes. Noticing that a portion of forest has been cleared by humans, Ursula steals a coconut that Noah planned to give to Rocco and Gertie as a wedding present and travels to the mainland with Chang and Mammothsbody to plant it. Upon arriving though, the animals meet Calanor, a devious aye-aye who hypnotises them into doing his bidding. Calanor commands the hypnotised Mammothsbody to take him to the Floating Island, where he plans to overthrow Noah as its leader, and things get worse for Noah when an enormous swarm of locusts descend on the Island and set about eating all the plants.

As the Island passes by Mauritius, Do-Dah is feeling depressed and frustrated about never meeting any other dodos in his life, and is in denial about his species' extinction. The Problem Walrus suggests that Do-Dah should visit Mauritius to find out more about his kind, and Sacha and Wommie accompany Do-Dah on his trip. Meanwhile, a sea turtle washes up on the beach and asks Noah and the Islander's help in defending her newly hatched babies from a hungry Komodo dragon.

The Island approaches the final leg of its journey, and Diamantina is only a few days away. However, a fire breaks out on a nearby island inhabited by giant tortoises. Noah commands one final rescue mission and the animals evacuate all the tortoises from the burning island. Afterwards, the Island finally reaches Diamantina, and the Islanders waste no time in disembarking onto the promised land. Upon arriving, the first animal they meet is Gorm, a woolly mammoth who turns out to be Salomi's long-lost father.