Yoshi's Island DS is a sequel to Super Mario World 2: Yoshi's Island and takes place after Yoshi's New Island. It's a time travel story where Future King Bowser and Future Kamek the evil Magikoopa travel to the past in search of Seven special babies known as the 7 Star Children who are born with extraordinary power and in the future will influence Mario's World: The Mushroom Kingdom. To prevent all of the later times Bowser, the Koopa Troop, and Kamek's Toady Army will face their comeuppance, they attempt to kidnap the babies from multiple different time periods.
This game has fewer (but also extended) levels, but has updated graphics, new babies (in addition to the returning babies Mario and Luigi), and a whole new adventure. The graphics still retain the trademark "pen and pencil" style of the original.
One of its new features is a museum of enemies in the game accessible at any time. In this museum all the enemies the Yoshis have defeated with Yoshi Eggs will appear here.
- Baby Mario – M Blocks can become stepping stones. A Yoshi can also dash at a great speed, allowing the Yoshi to escape from certain enemies. Yoshi can flutter farther than normal. His eggs bounce off walls.
- Baby Luigi - Kidnapped again just like in the original game. Luckily he hid in his blanket and wasn't spotted when Bowser and Kamek were checking the babies attempting to steal the Star Power from the Star Children.
- Baby Peach – With the parasol carried by Peach, Yoshi is able to flutter his way further and a bit higher. The parasol can catch wind currents. The eggs don't bounce off walls.
- Baby Donkey Kong – The current Donkey Kong's younger self. 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.
- Baby Wario – He carrying 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, his fire blast has the strength of an egg and the ability to melt ice, but his blasts don't bounce off walls.
- Baby Yoshi/Green Yoshi - The main character Yoshi that first appeared in Super Mario World (the playable Green Yoshi in the Yoshi games including the recent games Yoshi's New Island, Yoshi's Wholly World, and Yoshi's Crafted World and the same character as the Baby Green Yoshi from Yoshi's Story) who very frequently appears in the main Mario titles and it's subsequent spin-off titles such as Mario & Luigi: Partners in Time. Revealed at the end of the game, evidenced by him being picked up by the Stork and grouped together with the other Star Children, and in the last cutscene popping out of an egg (while still resembling an adult rather than the actual Baby Yoshis) revealing his Star.