When G'Bubu is hit on the head by a bongo nut, he assumes the personality of Peter Applebottom, a brilliant but pompous scientist who claims to know how to permanently fix the Core.

Allegra the crocodile admits to Zoe that she can't read. Zoe helps her to write a song for Animalia's talent contest. Iggy and G'Bubu also perform in the competition.

On a visit to his grandfather's home, Iggy must come to terms with the fact that he is not a full-blooded iguana, but rather, is part chameleon. With the help of his grandfather Carmine, Iggy gets in touch with his 'inner chameleon' and overcomes his fear of a recurring nightmare.

Tyrannicus starts his own nation of Tyrannia and teams up with the Creeper to declare war on Animalia, with the goal of driving Alex and Zoe out of the kingdom.

The search for the Creeper leads Alex and Zoe to the Chamber of Legends, a dusty room filled with Animalian relics. Alex reveals that he helped a weasel escape from the tunnels, and only now does Alex learn that the weasel is none other than the notorious Creeper.

Livingstone calls an Animalian meeting to reveal that the Creeper is back. He journeys into the tunnels with Alex and Zoe to find it. However, the Creeper uses the Wind of No Return to foil the heroes' attempts.

Iggy is asked to babysit Echo while his parents, Erno and Elni, handle a portal-guarding shift. To entertain the baby elephant, Iggy tells him tales of Animalia in which Iggy is cast as the hero. But the Creeper sweeps Elni and Erno into the tunnels in order to kidnap Echo, whom the Creeper believes stands in the way of him controlling Animalia.

Alex bets Zoe that she can't resist talking for a full day. It's a vow of silence. So Zoe spends the day listening to the amazing and magical world of Animalia, and makes new friends and huge discoveries.

When Alex and Zoe share a meal with the Horrible Hogs at the Elephants' Eatery they're appalled by the Hogs' awful table manners, crudeness, and limited social skills. The Hoity-Toity toucan overhears, and puts a spell on Alex and Zoe, making them Neanderthal versions of themselves.

A Corespore blasts off and flies to the land of Over and Beyond, where fictional characters live. With this Corespore missing, Animalians are unable to agree about anything.

Alex finds the Guardians of the Core Guidebook, which provides words and phrases that can help the Core. But when Alex isn't careful with the words he uses, the Core becomes a musical jukebox causing Animalians to sing and dance uncontrollably.

With the Creeper gone and peace restored to Animalia, Alex and Zoe decide it's time to go home. Livingstone also decides to take a much needed break, but before he can go, he must choose a new leader. Allegra and Tyrannicus vie for the position, but ultimately Livingstone knows that a good leader must lead with his heart.

After a few days in the 'real world', Alex and Zoe miss Animalia and want to return. But when they arrive, the city is in disrepair. They discover that time in Animalia moves at a different rate and a few days in their world is over a year in Animalia. Much to their surprise, G'Bubu and Iggy are no longer the leaders of Animalia, and instead King Tyrannicus is ruling the city.

The Creeper is back and he uses his knowledge of the Core to gain power and force the Animalians to do his bidding. Alex and Zoe are sent to protective custody, while G'Bubu and Iggy are searching the portals for Livingstone.