Baby Bowser – He can breathe fire, but the current Yoshi cannot swallow any enemies.

Baby Wario – He carries a magnet that attracts coins facing it (even through solid walls) and can move Magnet Blocks and Magnet Platforms.

The Yoshi Eggs do not bounce off walls, but they go faster and create a miniature explosion that can grab more coins and even defeat enemies. He can also do a DK Dash Attack, defeating most enemies. He can climb vines and chains, carrying the current Yoshi with him.

Baby Donkey Kong – He is the current Donkey Kong's younger self.

The parasol can also catch wind currents, and the Yoshi Eggs do not bounce off walls.

Baby Peach – With the parasol carried by Baby Peach, the current Yoshi is able to flutter way further and a bit higher.

Yoshi can also flutter farther than normal, and the Yoshi Eggs bounce off walls.

The current Yoshi can also dash at a great speed, allowing the creature to escape from certain enemies.

Baby Mario – He makes M Blocks tangible, and they can become stepping stones.

Babies can change places in Stork Stops inside levels. Most of the babies possess special abilities activated when the current Yoshi is carrying specific children. All the enemies the Yoshis have defeated with Yoshi Eggs will appear in this museum. One of the game's new features is a museum of enemies accessible at any time. The graphics still retain the trademark 'pen and pencil' style of the original Super Mario World 2: Yoshi's Island game. The game also possesses updated graphics and new babies (in addition to the returning babies Mario and Luigi from the previous game). Compared to the previous game, Yoshi's Island DS has fewer but extended levels. Usually, the Yoshis can target and throw Yoshi Eggs at the enemies to defeat them. In Yoshi's Island DS, the player takes control of many Yoshis traversing multiple levels and going through enemies, while carrying and protecting babies.

Future Bowser, Kamek and his Toady army attempt to kidnap the babies from the past. The game's story is about time travel where the King Bowser and Kamek, the evil Magikoopa, travel to the past in search of seven special babies known as the Star Children who are born with extraordinary powers and can be used to conquer the Mushroom Kingdom.

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