While Poof is practicing how to shapeshift, he is discovered by Mr. and Mrs. Turner who believe that he is an alien super baby that they need to raise to fight for justice and truth! Now Timmy Turner must find a way to get Poof back before his real identity is discovered, and Cosmo and Wanda cannot just wish Poof away because Timmy's parents have fallen in love with him!
When Timmy is teaching Poof how to shapeshift, Poof is getting everything mixed up, and isn't doing it right. When Timmy tells Poof to shapeshift into a tree, he turns into a bee, which Timmy says is okay because it sounds like tree. Wanda says he shouldn't be doing it out in the open, but Cosmo says that he used to be a terrible shapeshifter, then he says he'll turn into a ping pong table, but turns into a lion. Then some people from the zoo take Cosmo away, and then Mark Chang shows up and asks Timmy to fix his fake-i-fier, but then Mark is taken by the same zoo people, and Timmy continues on with Poof's shapeshifting. He tells Poof to turn into a bird, but Poof turns into a rocket and blasts away. Wanda is worried, and Timmy says it's close because birds and rockets both fly and have wings. Timmy and Wanda follow Poof to Timmy's house, where his mom and dad find Poof. Cosmo appears again, and Wanda tells him that they have their baby. They watch Mom and Dad take Poof into the house, where Timmy tries to take Poof away and "find" his real parents, but Mom and Dad take Poof, saying that they're his parents and that they need to take care of him until they find his real parents.
They name Poof "Super Baby", because they think he is an alien baby. Poof yawns, and Mom and Dad say that it's time for him to sleep, so they take out Binky's and (for some strange reason), put's them into their own mouths, where they fall asleep. And while they do that, Timmy takes Poof up to his room to Cosmo and Wanda, who are excited because they think their getting their baby back. Timmy tells Poof to change into a goldfish so he can go into the fishbowl with his real parents. He changes into a crab, which Timmy says is close enough, and tries to put Poof into the bowl. A portal is blocking Poof from going into the fishbowl. Timmy hears crying, and tells Cosmo and Wanda not to worry because he'll get Poof into the fishbowl. Cosmo and Wanda says it's not them crying. Timmy, Cosmo, Wanda and Poof see that it is his parents who are crying because 'Super Baby' is gone. Timmy's dad pulls out a picture of Poof saying that they loved Super Baby, then saying, 'Where did we get this picture?' Wanda then says that her and Cosmo can't get Poof back unless his parents give him up willingly. Timmy wishes for Poof to be on the couch with his parents, and for them to watch Poof until he can think of a way to get him back. Timmy's parents are happy because Super Baby is back. Timmy's dad takes Poof to the aquarium, which Timmy is mad because he asked his dad to take him there a million times, but Wanda gives him a mad look, and Timmy goes there to look for Poof.
Timmy finds his dad there, and asks him to 'willingly' give up Poof so he can 'bond' with 'his new baby brother'. So his dad does and he brings Poof over to Cosmo and Wanda, who are goldfish, and Cosmo and Wanda tell Poof that they really missed him, and Timmy tells Poof to change into a goldfish, but they see Mark and he yet again asks him to fix his fake-i-fier, but then a female octopus takes him and Mark can't break free. Poof seems excited by this and changes into an octopus, but Cosmo, Wanda and Timmy tell him not to. While Poof is a giant octopus, Timmy follows him over to the shark exhibit, where he tells Poof he is not an octopus, but a cute baby, so Poof changes back into a baby, but Timmy's dad finds him and takes him back home, and says that Timmy was jealous because he wasn't the only kid in the family (which isn't true).
Timmy's mom takes Poof to the super market for "super baby food". Timmy goes to the super market and tries to scare his mother into willingly giving up Poof, so he gets Poof to change into a monster, but it doesn't work. Timmy's mom doesn't see him and finds Timmy holding Poof next to a deli slicer, thinking it was another trick into getting rid of his godbrother. Timmy meets with Cosmo and Wanda outside, and she cries that she wants their baby. Timmy says he knows his mother will willingly give up Poof if she sees that she is breaking another mother's heart, and then Mark shows up again. He tells Timmy that he'll do anything if he fixes his fake-i-fier. Timmy gets Mark to dress up like an alien mother and to get Poof back, which he does, and Cosmo and Wanda are so happy that they have their baby back. Timmy wishes Mark's fake-i-fier fixed, and everything is back to normal. He then goes to his parents and his parents say that they only have one son, Timmy saying he is their only and super son. (Super Beaver) which the one of the hunters use a blow dart to shoot Super Beaver on the butt which now Timmy,Mr.Turner and Mrs.Turner sleeps.