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Baby Yoshi has returned to his herd in Dinosaur Land when a sudden chill comes over the area, it has never snowed before on this part of Dinosaur Island so they Yoshis flee in fear, they head towards the Vanilla Dome, a land completly inside a cave. They know that this area is inhabited by Birdos but they assume that they will be able to nest here. However scared that his tribe of multi-coloured Yoshis will not be safe Baby Yoshi calls upon the help of the other star children.
Level One - Yoshi's Island
Boss: King Freezem
Yoshi and his herd through the snowy area which has new foes that are like talking snowmen, they travel through the area defeating all of the new foes along the way. They find that their river has been frozen over in ice, they try to melt it with some firemouth from red shells, when they do they are attacked by King Freezem a giant snowman. When he is defeated they find the desert flower and star child Princess Daisy.
Level Two - Donut Plains
Boss Tyran O-Sore-Us Rex
The Yoshi herd and Baby Daisy continue through to Donut Plains which has not at all been affected by the strange snow of Yoshi Island instead it has been affectd by a severe drought and is being affected severly because of it. This does not please the Rexes who are usually very friendly with the Yoshis, it causes them to attack. When Yoshi, Daisy and the herd find their self-appointed leader Tyran O-Sore-Us Rex or "Tyrant" they have to defeat him, once they do so the Rexes thank Yoshi and his tribe and give him back someone that they found affected by the drough DK.
Level Three - Vanilla Dome
Boss Weather Staff
The yoshis arive in their thought to be safe haven with the Birdos the Vanilla Dome only to find that it has been flooded! The three star children try to find out what has happened here and they find the Birdo Herd has been washed away. They save the birdos and find a Magikoopa by the name of Weather Staff the first he has been the one that has been messing with the weather of Dinosaur Land under the order of the Magikoopa leader, Kamek. After he is defeated the three star children rescue his hostages Mario and Luigi. They decide that they can't move the Yoshis now they have to instead find Kamek and save Dinsoaur Land. The Yoshi herd stays with the Birdo herd.
Level Four - Cookie Mountain
Boss Kammy Koopa
The five star children proceed to move up along the Butter Bridge and find themselves on Cookie Mountain which has been the victom of an earthquake which has left the mountain in terrible shape. They find that the Monty Moles who live in the mountain are dieing because of the quake, the babies leave to find the cause of this and save the Monty Moles from extinction. They find that it is Kammy Koopa who they have met before as the nursemaid of Koopa Kid has caused the earthquake after she is defeated Princess Peach falls off her broom to the safety of the other star children.
Level Five - Soda Lake
Boss Buster Blooper
The six children find themselves coming off Cheese Bridge and not finding the large lake, but instead a dried up former river bed. They see that the bloopers, cheep cheeps and blurps either moved down stream or died. They continue through the lake on their way to the forest of Illusion where find a large Blooper who can survive out of water named Buster Blooper, in a fit of rage he attacks the star children. After his defeated the six babies continue through to the Forest of Illusion.
Level Six - The Forest of Illusion
Boss Way Out Wally
The six children see that the Forest of Illusion has been stripped of a lot of native flora because of extreme winds that are tearing up the landscape. The wigglers are extremelly angered by this, being a species that is noted to be easily angered this infuriates them, they attack the star children immediatly. As the children progress through the forest they find a Wiggler with Sunglasses on who calls him self "Way Out Wally" he is the self pronounced leader of the wigglers in this time of distress and he attacks the children. After he is defeated he lets out Wario who had fallen into the island and attempted to steal Wally's treasure, a giant Wiggler made of precious stones. The other children apologise for Wario and continue on.
Level Seven - Chocolate Island
Boss Patriarch O'Dino
The seven children find themslves on a completly unrecognisable Chocolate Island, it was once a rocky and mountainous area perfect for the Dino Rhinos however it has sprung into a forest grove filled with plants and grass, which to the most of Dinosaur Land would be great for the Dino Rhinos it is a curse, they can't graze or live peacfully like they were before. They are infuriated and blame the star children and attack them, when they find their King Patriarch O'Dino and defeat him battle he tells them that is all started when that crazy Magikoopa came over from the Star World. O'Dino shows the star children a star road so that they can access the Star World and fix up Dinosaur Land.
Level Eight - Star World
A normally peacful area with a few Star Yoshis however the Yoshis have all been expelled and it is hoarded with Koopa Troopas. The seven Star Children progress through the mysterious land to find Kamek and revert the island back to normal. When they defeat Kamek he still refuses to revert the Island back to normal, so Yoshi swallows up his wand, they hop on a star road and head back to Yoshi Island, when Yoshi spits up the Island is turned back to normal and so is the rest of Dinsaur Island.
- King Freezem - A snowman created by Kamek to destroy the Yoshi Island with a snow storm.
- Tyran O-Sore-Us Rex - A tyranical Rex who takes over the herd when it is danger, he attacks the star children when they come to the Donut Plains.
- Weather Staff - A Blue Magikoopa in a green robe who has been assisting Kamek and Kammy in chaning the land's weather and mixing up the Yoshis.
- Kammy Koopa - The old witch who signed up immediatly to assist Kamek in destroying the land. She takes Cookie Mountain to set up her domain.
- Buster Blooper - A Blooper who can survive out of water, he turned violent when his home Soda Lake dried up and attacked the Star Children blaming them for the incident.
- Way Out Wally - He is the prince of the Wigglers and after their forest is torn up he tells the wigglers to turn violent against everyone. Like most wigglers he has a temper.
- Patriarch O'Dino - He is the usually wise and peacful leader of the Dino Rhinos however when their land is destroyed thanks to the Magikoopas he is confused and attacks them. He then shows the star children the star road so they can enter the Star World.
- Kamek - The Magikoopa who attacks the Dinosaur Land to wipe out the Yoshi herd, he changes the weather and destroys everything before hiding out in the Star World.