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Baby Yoshi and the other Yoshis are sitting on guard at the eggs which they freed from Kamek when a pink egg begins to shake everybody believes it to be a Pink Yoshi and they sit in anticipation and wait for the egg to hatch only it's not a Yoshi it's a Birdo, a pink Birdo. The other Yoshis are disappointed and give her away to the Birdo tribe which shares the island with Yoshis.
Birdo feels dejected and leaves the island behind, Baby Yoshi wants to go after her but he can't because the other Yoshis wont let him. Baby Birdo finds Kamek who uses her as the new tool for Baby Bowser's scheme to revive his star power.
Birdo is brainwashed by Kamek who tells her that she can get revenge on the Yoshis that were so mean to her in the past, she is given an army of Shy Guys, Bomb-Ombs, Tweeters and Pidgits as well as a the Three Mouskateers (three Mousers). The brainwashed baby does as she's told and attacks Yoshi Island.
Yoshi calls upon his friends the star babies and they try to free Yoshi Island from the brainwashed Baby Birdo.
Level One - Distress Call
Baby Yoshi is alone and he sends out a distress call to the other Star children, he has to get through to the other side of the Yoshi City however to get to the beacon to make the distress call. He fights his way through the hoards of foes only to be attacked by a Mouser who calls himself Senor Mouser the First, he is the oldest of the three Mouser brothers and attacks Yoshi. After he is defeated he leaves gracefully.
Yoshi sends out the distress beacon to the other star children, immediately Baby Rosalina beams down to join up with the young Yoshi.
Level Two - Birdo Village
Baby Yoshi and Baby Rosalina continue down to Birdo village however they are not greeted as friends, the Birdos have sided with Baby Birdo and are attacking the two babies, they have to go through the village and disgrungingly defeat the confused Birdos.
When they reach the end of the level they find the village elder Catherine who has a lot of rings on her fingers and is very strong. After she is defeated she says that the village of the Pink Birdos will no longer attack them, she also opens up a crate which contained Princess Peach, she asks them if this belongs to them.
Level Three - Island Wilds
With Baby Peach joining their coup de tat the three babies continue through to the wilds of Yoshi Island where they are attacked by a group of the troups from Birdo and various other creatures. They also hear the call of the great ape himself Donkey Kong.
They rush towards the call only to be confronted by Senor Mouser the Second who is the middle child of the mouser siblings. After he is defeated by the three star children he releases a large heavy smelly sack and drops out Baby Wario, now reunited with Baby Wario and Baby Donkey Kong the babies head out for Birdo and wait for the Mario Brothers.
Level Four - Star Reuinion
The Babies continue through the island find themselves at the foot of Mt. Eruptus the volcano of Yoshi Island where the Red Birdo and Red Yoshi tribes live. These tribes are more vicious than the other tribes and do not side with them. They are attacked by the Red tribes and taken to their village.
They see that Baby Mario has been made their god and they are worshiping him in all of his redness, when he orders them to release his friends they turn against him and he too is attacked. Joining up with Baby Mario the star babies must defeat the red tribes and defeat their leader Yoshuprtus a large red Yoshi, Yoshi must do this himself.
After Yoshi defeats Yoshuprtus he vows his and his tribes allegance to the Green Yoshis, and thus unites all of the yoshis on the island. Yoshi asks the tribe if they have seen Luigi and they inform him that he has been taken by the Ravens.
Level Five - The Raven's nest
The six babies head straight towards Raven Woods where Luigi is being held, as they progress through they see many different kinds of Ravens even some ravens that can fly! When they reach the centre of the woods they see the meeting place of the ravens where they all stand around and worship a giant golden Raven statue which they believe to be their god.
They are about to sacrifice Luigi to the idol when the babies jump in and attack the ravens, they free Luigi and melt the statue which angers the Ravens, they then scatter out of the forest.
Level Seven - Baby Birdo's Baby Shrine
The seven continue through and they find a palace which has already been erected dedicated to Baby Birdo as if by Magic, when they get in there they see that it has indeed been created by magic as there is several Magikoopas around the palace. The babies continue through the palace and wipe out the magikoopas and other baddies that are hiding through the palace.
When they are about to leave the palace they are confronted by Senor Mouser the third the youngest but strongest of all the Mouser brothers. He attacks the babies and when he is defeated says that the great Magikoopa hypnotised the poor baby.
Level Eight - Baby Brawl
The babies find the makeshift castle on Yoshi Island which is the base of Baby Birdo who they now know to be hypnotised so they try not to hurt her too much, just snap her out of her hynotysm. However all through her castle are very tough foes and a group of angry Ravens trying to get revenge on the babies.
When the defeat Baby Birdo she snaps out of her daze and cries, she can't identify the one who hypnotised her but she goes back to a life amongst the Pink Birdo tribe happily.
- Baby Mario - Playable after level four "Star Reunion"
- Baby Luigi - Playable after level five "The Raven's Nest"
- Baby Peach - Playable after level two "Birdo Village"
- Baby Wario - Playable after level three "Island Wilds"
- Baby Donkey Kong - Playable after level three "Island Wilds"
- Baby Yoshi - Playable from the start
- Baby Rosalina - Playable after level one "Distress Call"
- Mouser Brothers - Kamek leaves these three brothers in charge of protecting Baby Birdo and making her stronger to take over the island.
- Baby Birdo - Not actually a villain as she was hypnotised by Kamek however she is the final boss of the game,
- Kamek - He is not fought in the game but he does appear as an enemy. He hynotyses Baby Birdo into doing evil and give her an army of minions.