When Timmy wishes up a baby for Cosmo and Wanda to fulfill their never-ending desire to be parents, the Anti-Fairies and the Pixies join forces to use the baby's untapped magic to take over the universe. It's up to Timmy, Cosmo, Wanda, and Jorgen to make sure the first fairy baby born in 10,000 years is safe with its new family.
Timmy can't do anything when Cosmo and Wanda are distracted by the baby stuff, because they want their own baby. The problem is, since Cosmo was the final fairy baby born and he destroyed Fairy World by turning Jorgen into a bomb, the Supreme Fairy Council forbids fairies to have any children. Timmy gets really fed up with them crying and ignoring him because they want a baby. He then notes to himself it wouldn't be so bad to have a godbrother/godsister and also figures that he can just wish up a baby for his godparents. Wanda notes to Timmy "You can't just wish us up a baby.", but then questions "Can you?". She then poofs up Da Rules to see if Da Rules forbid godchildren for wishing up any more fairy babies. Timmy then reads Da Rules himself, but doesn't find anything in it to forbid godchildren from wishing up fairy babies, so he believes that wishing up a fairy baby is okay. But just as he was about to wish for one, they are suddenly poofed to Fairy World by Jorgen who yells out "Stop!". Jorgen notes he had sensed the disturbance in the Fairy Force because someone was just about to wish for the "B-word"; he is scarcely surprised that it was Timmy, who points out that there's nothing in Da Rules that says he can't wish for the "B-word". Jorgen tries to prove him wrong by looking through Da Rules again and finds out that he wrote this rule on a sticky note, but never officially put it in. He lets Timmy make the wish, but tries to warn him of the consequences, though Timmy doesn't care. He then makes the wish. Just as there is a big poof, nothing seemingly happens. Jorgen corrects that his wish will come true, but warns that this is only the beginning. He then shouts at Timmy for interrupting him in the middle of sentence and tells him go. Jorgen also breaks the fourth wall, telling Timmy and his fairies to go as the camera zooms in on him dramatically. It soon gets too close to his face, so he tells it to back off.
So for the next three months, Timmy eagerly waits for his soon-to-be god brother or sister. Surprisingly, he learns that Cosmo is the "mother" and has to deal with wild mood swings, weird cravings and continuous barfing. As it draws near for the baby to be born, many fairies host the baby shower in Timmy's bathroom. The fairies reasoning is that the bathroom is the most private room in the house; Jorgen further asserts that he doesn't want news of the new fairy baby to get out yet, for in its earliest stages, fairy baby magic is powerful and unstable. He explains with a slideshow that if the baby is raised by a good fairy, its magic spreads goodness; when raised by an Anti-Fairy or Pixie, the baby's magic can be used for evil, as well as destroying the Earth. He then ends his explanation by stating that the party should go on. Unfortunately, Timmy, as the host, is subjected to a variety of dangerous games. He gets so tired of Cosmo with his cravings, barfing, and mood swings, that he wishes that Cosmo would just get lost. An insulted Cosmo complies and poofs away (also taking his unborn baby with him). Jorgen admonishes Timmy for such a reckless outburst, for if the Anti-Fairies or Pixies get the baby, it'd be so bad that he would have to make up a new word: Doomungous. Timmy apologizes, saying that he really does want a fairy god brother or sister, but he was sick of Cosmo's barfing. Jorgen then dispatches all the fairies to search for Cosmo, as he turns the bathroom into a military-coordination room. Unfortunately, searching all over the Earth turns up nothing. Wanda says that there are other worlds they can check. Wanda suggests Anti-Fairy and Pixie World, and Timmy claims that the Anti-Fairies kidnapped Cosmo and that they need to go get him.
In Anti-Fairy World, Anti-Cosmo asks his anti-fairies for a plan for universal domination (Quoting "There's no wrong answer"). One anti-fairy suggests using a pink elephant to storm on others, causing Anti-Cosmo to sent him down a trapdoor. He encourages the others to think of a plan, stating, "A plan for universal domination isn't just going to come bursting through that door." At that moment, Timmy, Wanda and Jorgen, armed with bazookas, demand to know where Cosmo is. Unfortunately, they inadvertently alert the Anti-Fairies that the Fairy Baby can accomplish their goals. Wanda, Timmy and Jorgen then go to Pixie World, where the Pixies have come up with the same plan as the Anti-Fairies, only to alert them too.
While Jorgen goes to the washroom for eating so many hot burritos, Timmy and Wanda realize that Cosmo actually got lost, and find him in a meadow. So after apologizing to Cosmo, Cosmo's belly pushes them away, and Cosmo goes into labor. They take him to the Fairy World hospital, and they find out that nobody knows how to deliver a baby, for it hasn't happened for thousands of years. So Timmy wishes the baby out, and when Cosmo opens the blanket when they baby appears, it reveals a really cute baby, saying its first word, 'poof'. When they try checking with gender the baby is, Dr. Rip Studwell tries taking the baby outside where the light is better, only for Jorgen to suddenly appear, revealing the doctor to be Anti-Cosmo in disguise. Jorgen then tries leaving, only for Anti-Cosmo to reveal that the Pixies are riding another Jorgen suit. Mama Cosma then snatches her grandchild from them and attempts to go outside, only for the real Jorgen to arrive, attempting to expose her as an impostor, only to find that it's really her. Wanda then takes back her child, trying to passionately defend that only she and Cosmo can truly care for it, only to find her child gone. Timmy, obviously hiding the baby under his shirt, tries saying that they should all go outside, only for the baby to say, "Poof poof." Everyone hears this, and Jorgen, Anti-Cosmo, the Pixies and Mama Cosma gang up on him, demanding the baby for their own purposes.
Timmy attempts an escape with an ejection bed, only to get himself and his fairies slammed into the wall instead of through the door. As everyone else comes charging, the baby starts laughing, causing its parents and Timmy to disappear for a moment, while their chargers ram into the wall, before going outside, where they find that the light is better; the baby's laughs causes good things to happen. Timmy tries wishing up a rocket van for their escape, though Wanda insists on a stroller. Jorgen, Anti-Fairies and Pixies give chase in jets (everyone asks why are they in jets when they can fly; Jorgen says that he thought it would be fun; he also ejects Mama Cosma for her constant nagging). Timmy and co. take cover in a deep forest, only for Cosmo to freak out at their scary environment, which in turn, causes the baby to cry. This causes the woods to disappear and a big sign to show their location, which everyone else finds due to their convenient sensors; also, the baby's burp causes lightning. Timmy then insists that his fairies send him to back Earth with the baby, whom he names Little T, for Little Timmy, while they take decoy dolls to lead the others off the trail.
When Timmy arrives back on Earth, he finds his parents in jog wear to stave off aging; they all think Little T is a doll and smell the new baby smell. Timmy then takes the baby on a stroll in the park, while talking about all the things they will do. However, the baby's laughs and cries causes both joy and chaos for everyone around them before it is pacified by its bottle. Worse, it then hiccups, causing natural disasters. Jorgen turns up and repairs the damage before demanding the baby, pointing out all the damage it has caused. Timmy initially refuses before being struck by lightning, only for "Jorgen" to be reveal to be Anti-Cosmo and HP in another robot suit. They explain that they have decided to work together to use the baby's magic for evil and poof away. Then, the real Jorgen, having captured Cosmo and Wanda, appears to gloat about his foolish trick, only to learn about the baby being in the hands of evil.
With Wanda's maternal instincts, they track their quarry to Anti-Fairy world. Timmy then comes up with a plan. The next scene shows Timmy dressed as a knight, Cosmo a Mexican food delivery boy (note the restaurant he's promoting, Taco Town, is a parody of Taco Bell.), Wanda an archer and Jorgen in a pink bunny suit, all captured in a giant butterfly net. Anti-Cosmo and HP, holding their foes' wands, gloat about their victory. Once they are left alone, Wanda blames Timmy for wishing up the baby in the first place, before breaking down crying, wanting her child back. As Cosmo comforts her, Jorgen further scolds Timmy for such a terrible plan, breaking a woman's heart, essentially dooming the universe, and worse putting him(Jorgen) in a bunny suit. However, Timmy insists that his plan isn't finished yet and uses his sword to set themselves free.
They then find Anti Cosmo and HP, who are in the process of draining the baby's magic and using it to destroy both the Earth and Fairy World. Timmy has Wanda fire a milk bottle with her bow into the baby's mouth, causing its burps to shock Anti-Cosmo and HP. He then uses Cosmo to fire his earwax at the other Anti-Fairies and Pixies. Then, Jorgen is ordered to dance, at which the baby laughs, causing the sky above their heads to rain bunnies. Subsequently, Timmy slams a mace on Jorgen's foot, causing him to yell out in pain, which, in turn, made the baby cry, forming the other bunnies into a ferocious, evil rabbit, which destroys the giant wand. The last part of the plan was for the baby to eat a burrito, which everyone fears could be disastrous if it breaks wind. As what they predicted happens, reality is warped and soon, everything is restored to normal. Jorgen compliments Timmy for saving the universe from the Anti-Fairies and Pixies, who have all been turning into raisins. He then takes the baby, whom he names Napoleon, into his custody, stating that they can see him every other century, as well as a magic rattle to enable it to control its magic. But in truth, Cosmo and Wanda replaced the real baby with the fake baby. So when they take the baby home, they discover that their baby is a boy, because he's holding a water squirter (According to Timmy boys love water squirters). Timmy then names him Baby Poof, because it's the only word he says. Poof then goes flying around, transforming everything in sight, before the house sprouts legs and starts running, with Timmy's parents chasing after it. Mrs. Turner notes the house has the new baby smell as the episode ends.