Baby Bowser is jealous of the Yoshis and their Super Happy Tree, responsible for spreading joy over Yoshi's Island. He steals the tree and hides it in his castle, making all the Yoshis sad and unwilling to rescue it. Luckily, six baby Yoshis are born, all of them happy and surprised to see the older Yoshis so sad. They decide to team up and travel to Baby Bowser's Castle to save the Super Happy Tree and restore happiness to the island.
The aim is to reach Bowser's Castle by travelling across six pages of a story book. Each page has four stages, but you only need to complete one stage at a time. To complete each stage, you have to eat 30 pieces of fruit, which can be found all around each stage.
In the corner of the screen is a Flower Meter that shows you your health. You can restore health by eating Fruit. Each Yoshi has a favourite fruit depending on its colour (eg. Yellow Yoshi likes bananas best), which provides more health than other fruits. Before each stage you also pick a Lucky Fruit that provides extra health. Heart Fruits and the special Honeydew Melons provide all Yoshis with a lot of health.
As in Yoshi's Island, you have to eat enemies to turn them into eggs, which can be used as weapons. Using the N64 analogue stick, you can more accurately aim the targeting reticule. Eggs don't bounce as before, but will explode in a firework when they reach the target you specified, damaging any enemies or breakable areas around it.
In order to unlock more stages on the next story book page, you have to find the three Big Hearts hidden around the stage. Each stage also has 30 Honeydew Melons to find. Try finding all 30 Honeydew Melons in a single stage for an extra challenge.
As well as the Story Mode, there is also Trial Mode, where you can play any of the stages you have completed in Story Mode. The aim in these stages is to get a high score, with certain enemies and items worth more points depending on whether their colour matches that of your Yoshi.