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Peach had to think about Bowser Jr.'s statement because...
  • She actually did have an affair with Bowser at some point. It's possible that she even did carry another child of his, whose whereabouts are unknown. Given the... disputed nature of the Koopalings' parentage, their real child is probably one of them. Probably Wendy, who even appears to have inherited some physical features from Peach, such as her blue eyes and large lips. In short, she did give birth to one of Bowser's children; she just doesn't know which one.
    • One problem: Miyamoto stated that the Koopalings are not Bowser's children. While that doesn't joss the possibility of Peach and Bowser having an affair at some point, it does make it less likely that Peach had one of his kids (unless it turns out that Wendy Koopa is actually related to Bowser).

The reason Peach didn't outright refute Jr's statement.
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  • Is that contrary to the above, she was just stunned. Honestly, a dinosaur/dragon/turtle half your size kidnaps you and claims that you're its mother. Even if you are kidnapped semi regularly by a similar turtle/dragon/dinosaur, that's gonna take some time to process. The sheer absurdity makes her wonder what the hell this boy is on about.

Alternatively. to the above...
  • Peach has no idea how children actually are born (remember this is a world where the stork delivers babies) and is considering that Bowser Jr. literally is her child somehow.

The reason Bowser claimed Peach was Bowser Jr's mother is quite simple
He was planning on having Peach become Bowser Jr's adoptive mother.

As we see in Super Mario Odyssey, Bowser kidnapping Peach to marry her is something he'd be willing to do. However, instead of going straight to the marriage, this time he was hoping that he could trick Peach into growing close to Bowser Jr, and wanting to raise him, then after that, he'd pop the question, saying "Since you want to be his mother, why not make it official?" (or something along those lines). In other words, he was hoping that he could cause Peach to develop a case of Stockholm Syndrome - he didn't specify when Peach would become Bowser Jr's adoptive mother because that would ruin his plan.

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Bowser Jr. is a Child by Rape
Think about it. It would be far more in character for Bowser to finally snap after so many rejections from Peach and force himself on her during one of her stints in the castle. As for the pregnancy, depending on how long Mario takes to rescue Peach, she may have already given birth by the time Mario arrived. Peach then represses the memory of what happened, hence her surprise when Junior calls her Mama. As for why Bowser later states she isn’t Junior’s mother, he’s trying to protect his son, since he feels he crossed the Moral Event Horizon with Peach when junior was conceived and he knows junior idolises him, so he doesn’t want to tarnish his relationship with his son. He also doesn’t want junior to make the same mistake and let a moment of blind rage lead to him taking things way too far. Junior knows his father is lying, but just plays along because he knows Bowser must have his reasons. The reason he knows Peach is his mother is because he overheard Bowser saying so during a private conversation with Kamek.

The Piantas are color-blind.
  • This could explain why they couldn't tell the difference between real Mario and Shadow Mario.
    • And how one Pinata explorer you meet in a bonus level has difficulty finding the Red Bird of Happiness for almost forty years while Mario found it no sweat.

The whole game was an inside job, set up by Isle Delfino's government
Hear me out. Throughout the game you encounter citizens in possession of Shine Sprites. Some give them to you in exchange for a favor, some hand them out as prizes, and two certain raccoons sell them for blue coins, but despite being so important to the well being of the island, none of these citizens ever hand them over to you or the government for free. Why be so stingy in a time of crisis? Because the government of Isle Delfino is corrupt, and hoarding Shine Sprites is the only way the citizens can keep them in check. Without Shine Sprites of their own, they would have no control.

Of course, the government doesn't like this one bit. They want all of the Shine Sprites in their possession. But they can't just go to war on the people. So what do they do? Get Mario.

Why do you think Mario was named guilty when, even if you couldn't tell the difference between Mario and Shadow Mario, there were several witnesses that could vouch that Mario only just arrived? Because they were framing Mario. In fact, the entire situation with Bowser Jr. was set up by the ruling body themselves.

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They heard about Mario's adventure from Super Mario 64. They heard how Bowser had stolen all of Princess Peach’s 120 Power Stars, and how Mario got them all back. Coincidentally for them, there are also 120 Shine Sprites. That's when they got a brilliant idea: they would get Bowser to 'steal' all of the government controlled Shines, and then Mario, not knowing about the situation, would collect both the government and citizen-owned Shines for them, thus putting all 120 in their control.

Getting Bowser on board was easy, a simple payment and a chance to get revenge on Mario was all he needed. But how could they get Mario? Sure, Bowser could have just kidnapped the Princess and lured him to the Island. Mario may have still collected all of the Shines. But what if he decided to just leave? Or worse, what if he decided to give everything he got to the citizens? For the plan to work, Mario had to be kept under government surveillance and forced to stay until every Shine was given to them. They needed to make him a prisoner, so they decided to frame him. That's where Bowser Jr. came in.

For years, Bowser had lied to his son about Peach being his mother and getting kidnapped by Mario. Bowser Jr. was eager to fight Mario, so Bowser had a magic bandanna made for him so he could transform one of their minions into Mario for practice. When the idea of framing Mario came up, Bowser realized that Jr could instead wear the bandanna himself and act as an impostor committing crimes under Mario's name.

But Bowser Jr. was still young and weak, he required a tool of sorts to do this. They heard word of Professor E. Gadd's unethical work into living paint. Something like that would surely work for Jr., so they commissioned Gadd to build Jr. his Magic Brush. But what was to keep the paint from getting out of control? They needed a weapon for Mario as well. Wasn't it convenient that the F.L.U.D.D., another invention of E. Gadd and the perfect tool for fighting the paint just happened to be on the same runway Mario arrived on? Wasn't it also convenient that nozzles for F.L.U.D.D. could be found all over the island, despite there being no signs of other F.L.U.D.D.s there? The government placed the F.L.U.D.D. and all of its nozzles carefully around the island for Mario to use.

The last thing to do was lure Mario to Isle Delfino, and what better way than a complementary vacation? Mario and Peach certain deserved one after dealing with Bowser so many times. Plus, with Bowser in their pocket, the Mushroom Kingdom could be kept safe while they were gone. They contacted Peach, booked their trip, and set the plan in motion.

So Bowser Jr. ran amok on Delfino, Mario arrived and was arrested, and then the Shine collection began.

This is the true reason why collecting every Shine is disappointing. Not because of the hardships, not because of the post card, but because you aided a corrupt government in fully subjugating their people. Thanks, Mario.

  • This would explain a lot of the game's oddities, such as why it only takes fifty out of one hundred twenty shines to reach Corona Mountain but only if those fifty were found in a very specific and not at all specified order. And someone around the time actually working for Nintendo may have felt the same way, as the Piantas are the most open and politically powerful criminal element of Paper Mario: The Thousand-Year Door.

After this game, the Mushroom Kingdom conquered Isle Delfino.

Possibly as a corollary to the above. Peach may have enjoyed her vacation to the island, but she and Mario can't have been left with a good impression of its leaders. So, once they got home, Peach declared war in the name of regime change, and took the island over herself. This is why there's a beach named after her on the island in the Mario Kart games.

Contradicting popular opinion this game is actually an Immediate Sequel: to Luigi's Mansion, not a prequel
  • Since that's ABSOLUTELY NOT King Boo and it would explain why Luigi isn't there...
    • Popular opinion? The idea that this game is a prequel died years ago. Being a sequel to Luigi's Mansion is practically canon judging from the line "Why can't some suck up all these ghosts with a vacuum? What, why are you looking at me like that?".

The five toads that accompany Princess Peach went on to become the Toad Brigade.
The red one decided to make himself the leader and call himself Captain Toad. As for the blue one wearing glasses, and the yellow one sleeping a lot, maybe the blue one just wasn't wearing his glasses that day, and the yellow one doesn't always fall asleep all of a sudden, either...

At some point in development, there was an ice world planned
In Super Mario 64, there were 2 ice worlds. And in the next 3D Mario Platformer, Super Mario Galaxy, had 2 ice worlds. Yet Sunshine has no ice world. It's likely that they had planned an ice world at some point, but scrapped it due to a), the tropical island setting making it hard to justify a cold level, and b), FLUDD would not be as useful due to his water freezing (and the fact that they would have had to have made a Flamethrower mode for FLUDD if this was the case), the level was scrapped before it was programmed.

Bowser Jr. is actually a lab grown clone.
He was made with Genetic Samples from Bowser and Miyamoto, probably as payment to bowser for his help with the shine sprite plot.

King Boo looks different in this game because of the events in Luigi's Mansion
At the end of Luigi's Mansion, King Boo is sucked up by the Poltergust and turned into a painting, a state he doesn't escape from until years later, in Luigi's Mansion: Dark Moon. During this time, someone else had to take up the role of King Boo. The King Boo we see in this game is likely a relative of the real king, taking over until King Boo eventually escapes.
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