Bowser Jr. invades Yoshi's Island.
A Yoshi can morph into several different types of vehicle with the help of a Morph Bubble. Morph Bubbles appear many times in the game. There are three forms:
Helicopter: The helicopter is able to make a Yoshi fly for a short time.
Submarine: The submarine can make a Yoshi swim underwater (Yoshis in the game, can't swim underwater).
Mole Tank: This tank makes a Yoshi able to dig through small openings and dirt.
To turn back into a Yoshi, the Yoshi must either touch a Yoshi Block or wait until a little while and time runs out, as the forms only last for a few seconds. However, when the Yoshi is turned back into a dinosaur, he will also return back to the Morph Bubble if he fails to reach the Yoshi block in time. Additional forms from the original game like the train and the car forms were cut out from this sequel.
Yoshis can also hop into or onto various vehicles. There are five vehicles:
Kangaroo: The Kangaroo hops on its own, but pressing and holding left or right tells which way the Kangaroo should go, and how far it should go. Also, holding the A button will let the Kangaroo float.
Stilts: Hopping on stilts allows the Yoshi to walk around in the same manner as the Stilt Guy does.
Carts: Hopping in a cart makes it roll along a track on its own. Players cannot change the direction.
Skis: Found in some ice-and-snow levels, players cannot change the direction of skis; however jumping is possible.
Rocket: Some huts lead to space launch pads, allowing Yoshi to hop into a rocket and blast into space. Pressing left and right turns the rocket and Y gives extra thrust.
Any Flowers the player collects in a level will appear in the Goal Roulette at the end of a level. After a Yoshi passes through the ring, the spinning will get slower. If it stops on a flower, the player will be able to play a mini-game and probably earn 1-Ups. There are five different flowers in each level-here is a list of the Mini-games that may pop up if Yoshi is able to get a flower in the Goal Roulette.
After the events of Super Mario World 2: Yoshi's Island, Kamek and his evil army of Toadies decide to steal all of the babies in the Mushroom Kingdom, as well as other nearby areas. The Toadies are taking the babies to a mysterious floating castle by Kamek's lead. The Stork comes in and attacks two Toadies making them drop the babies they are carrying; The two babies then land on Yoshi's Island. It appears to the Yoshis that these two babies are Baby Mario and Baby Peach.
The Yoshis find the babies, and decide to help them. The Yoshis figure out that Baby Mario, once again, wants to save Baby Luigi and the other babies from Kamek and his Toadies. The Yoshis take the babies with them, and go on an adventure to rescue the kidnapped babies. Later on in the adventure, a group of Ukikis kidnap Baby Peach.
The Yoshis and Baby Mario find another baby, Baby Donkey Kong; The baby ape was somehow left behind when the Toadies were kidnapping all the other babies. With the help of Baby Donkey Kong, Yoshi is able to rescue Baby Peach from the Ukikis. After his helpful act, Baby Donkey Kong joins the team. Quite some time after that event, the Yoshis also find Baby Wario, who like Baby Donkey Kong, was left behind; Baby Wario decides to join the party.
After being with the gang for some time, Baby Wario decides to instead join a team of Bandits, because Wario is very greedy as are the Bandits. It is revealed after beating Priscilla the Peckish that the future Bowser and future Kamek are looking for seven Star children, young children that have magical stars in them. If someone collects all the stars, then he or she will rule the world.
It is soon discovered that Bowser and Kamek are kidnapping the helpless babies in hopes of finding the seven that have stars within them. Kamek, using a Crystal Ball, checks every baby they have kidnapped (with the exception of Baby Luigi who was hiding) but finds out that none of them have the star inside of them. Bowser grows angry and sends the Toadies to keep looking for more babies.
After the Yoshis continue the adventure, they find Baby Bowser. After a fight between Baby Bowser and Bowser, Bowser threw Baby Bowser out of the castle. Baby Bowser complains to the Yoshis that his future self is stupid, and decides to join the Yoshis, even though the Yoshis are worried that Baby Bowser might suddenly attack them. However, Baby Bowser does not stay for the whole adventure; Later in the game, he leaves with Kamek.
At last, Yoshi and the babies arrive at Bowser's Castle where all the babies come back to help Yoshi travel through the castle. However, when they finally get to the top of the castle, Baby Bowser tells the Yoshis to leave. However, when they don't leave, Baby Bowser thinks Yoshi is there to steal his treasure. Baby Bowser fights Yoshi but Yoshi defeats him.
Bowser then comes in the room and is angry at what Yoshi did to his younger self and fights Yoshi but gets defeated, just like his younger self. However, Kamek helps Bowser to become Giant Bowser. Giant Bowser and the four babies with four Yoshis fight against the Giant Bowser using Giant Eggs and are eventually able to defeat him. After Bowser is defeated, Kamek escapes, with four Toadies carrying the defeated body of Bowser right behind him. Baby Bowser decides to escape with Bowser and Kamek too, and holds on to his flying broomstick.
The Yoshis save all the kidnapped babies, and the stork takes all the babies back to their home, except for Baby Wario who is homeless. Supposedly, the Stork adopts Baby Wario and takes him to a raft where Baby Bowser's treasure ended up. Meanwhile, a flying rock hits Kamek's broomstick, and Baby Bowser lets go of the broomstick. He falls down right in his treasure where Baby Wario and Baby Bowser start arguing about who gets to keep the treasure.
It is then revealed that the seven Star Children were: Baby Mario, Baby Luigi, Baby Peach, Baby Donkey Kong, Baby Wario, Bowser and a newborn Yoshi, who had just hatched from his Yoshi Egg at the end of the game.
For each of the three player files available, there are four modes to choose from: Adventure, Mini-games, Time Trial (unlockable) and Options.
A long amount of gameplay comes from adventure mode, similarly played out like the original. Throughout the five unique worlds, a different colored Yoshi takes on one out of eight levels, with a mini-boss in Level 4 and a boss in Level 8 of each world. Enemies, items, and coins litter the levels, as well as collectibles. When a Yoshi is hit by an enemy, the baby is knocked loose from his or her back, and the Star Power – the source of the protective bubble that keeps the Toadies from taking the baby – goes down by one star per second. If that number goes down to 0, Toadies take the baby and a life is lost. The star power starts at 10 in each level, and if a baby is recovered with less than 10 stars, the star power automatically goes back to 10 again at a slow recovery rate; the star power maxes out at 30. Groups of 5 stars often come in Winged Clouds and Crates.
There are various Mini-games to be unlocked in Adventure Mode: Tulip-Shooter, (a mini-game where Yoshi must eat enemies and spit them out into a tulip), Flutter Challenge, (a mini-game in which Yoshi must try to flutter-kick as far as possible), Bouncy Maze, (a mini-game where Yoshi must maneuver his way through a simple maze of Bouncies), Speed-Eater, (a mini-game where Yoshi must try to swallow as many enemies as possible), Flip (in which cards can be flipped over to earn 1-ups), and Egg Toss, (a mini-game where Yoshi must hit targets with eggs); all mini-games have a set time limit. Achieving a high score in any mini-game will award the player with a 1-up. Harder versions of all the mini-games can be unlocked by collecting all the Baby Coins in a world.
Unlockable once Adventure mode has been beaten, Time Trial is just like Adventure mode, however the player is timed. The player has one-hundred minutes to finish the game – even when the player presses the Start Button, the time keeps going.
New to the sequel at certain spots are Stork Stops, which let Yoshis change babies, providing different unique abilities:
Baby Mario: M Blocks become tangible, providing stepping stones. A Yoshi can also dash at a great speed, allowing the Yoshi to escape from certain enemies. Yoshi can flutter far and normally.
Baby Peach: With her parasol, Yoshi is able to flutter further and a bit higher, but also a bit shorter than Mario. Her parasol can fly wind currents up or down; her eggs don't bounce off walls.
Baby Donkey Kong: He can climb vines and chains, carrying Yoshi with him. He can also do a DK Dash Attack, defeating most enemies. His eggs don't bounce, but they go faster and create a miniature explosion that can grab more coins and even defeat enemies or activate winged clouds just blocked off by solid wall.
Baby Wario: He is accompanied by a magnet that attracts coins facing it (even through solid walls) and can move Magnet Blocks and Magnet Platforms. His eggs will bounce off of walls.
Baby Bowser: He can breathe fire, but Yoshi cannot swallow any enemies. Often, though, a fire blast is the equivalent of an egg,being able to break winged clouds and destroy dirt walls as well as melting ice, but the blasts don't bounce off walls.