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E. Gadd designs Andrew and Andrea to be normal robots and not able to shut down with the other Anderobots. He creates a new good robot called A.B.C.. Baby Mario gets the robots to do EVERYTHING for he, even change his diaper! Needless to say he has become very lazy leaving most of the heroic duty around the Kingdom for the other six star children, much to their annoyance.
Koopa Kid waits one more year to get his revenge, he was angry at his cousin Baby Bowser for making him loose his Nega Star Power and he is angry at the Star Children for defeating him, he waits in the shadows with his new ensemble team of Kamella, Kammy Koopa and Petey Piranha to defeat the children once and for all.
Seeing how much Baby Mario had exploited his power he strips him of his star status and gives it all to Baby Bowser out of rage. Baby Bowser is overcome with glee and power and he kidnaps all of the star children, aside from Baby Yoshi who is back at home with his friend Baby Birdo.
Koopa Kid meanwhile has his two Magikoopa friends Kamella and Kammy Koopa create a new more powerful Star Power called the Ztar Power, which makes Koopa Kid near unstopable and so he too wants to extract his revenge on the Mushroom World.
Baby Yoshi and Baby Birdo traverse to Bowsers Keep and one at a time they free the other Star Children who now begin to remember that they are the heroes and they have to stop the two villains, the Grand Star is very pleased and he returns the star power to the seven children, Baby Bowser attempts to flee however he falls into lava and rises out as Baby Dry Bowser, he attacks the children only to loose, he has Kamek return him to normal and he then flees.
As the babies (minus Baby Birdo who returns home) find Koopa Kid and defeat him once and for all, the Ztar power that Koopa Kid once possessed is turned into another Star Power and disappears into another star child, a cut scene shows Baby Funky, Baby Rosalina, Baby Toad, Baby Birdo and Baby Toadette however it is not revealed which of the children receives the star power. The game and the series then draws to a close.
Mario & Luigi: Partners in Time (real game) continues where this game left off, however no mention of the star power is made, it is still not revealed which of the four children became the fourth star child.
- Baby Birdo - Until Bowser battle
- Baby Yoshi
- Baby Peach
- Baby Mario
- Baby Luigi
- Baby Wario
- Baby Daisy
- Baby Donkey Kong
- Anderobot X
- Gigamechamadkid-M.E.G.A Type
- MEGA TOAD X
- PARA-ANDRO TROOPA
- S.T.O.M.P. the Goomandro
- F.L.O.A.T. the Blooperbot
- Anderobomb the Bob-omb