- Why do Mega Evolutions go berserk after a certain point? That's because they're using a whole untested different method and they lack a human partner and the necessary items to control it. At no point does the story ever refer to Mega Evolution as an important thing as well, probably because of the side effect.
- The Partner being afraid of ghosts is a common childlike trait. But then we know that the Partner is an aspect of Mew, who is a Psychic Type. The type that is weak against Ghosts.
- Nuzleaf doesn't appear to be mad at the player character for going into dangerous dungeons, in fact actively encouraging them to explore wherever they'd like. Could be his lax nature as a parent... or the fact that Possessed Nuzleaf wants them to get stronger and more Dungeon savvy so that they would be able to survive Revelation Mountain.
- Your partner's capricious personality seems a bit different from the partners from the other games; they're willing to break rules they don't like and they don't seem fazed at all when a threat comes their way. This is because that's how a Mew acts, going from the other Mew we've seen.
- Jirachi seems to brush off how the player character was a human, saying it "happens all the time." If this Jirachi is the same as the one from Pokémon Mystery Dungeon: Explorers, then he's already seen a human-turned-Pokemon before.
- Ninetales, who's implied to be the same one from Pokémon Mystery Dungeon: Rescue Team, says they know of "others" who used to be humans, when meeting you. Note the plural. The other one is Gengar.
- In the fight with the illusionary Giratina, it has Hidden Power, Protect, and Safeguard. All moves learned by Solosis at a low level or by TM. It turns out that a Solosis is responsible for the illusion.
- Rayquaza suddenly Mega-Evolving to stop the Tree of Life from escaping the planet makes perfect sense when you consider that in the main series it doesn't evolve from outside assistance via a Mega Stone or an Awakening emera, but from the hopes and wishes of everything around it. Of course it's going be able to enter it's super form; practically every single remaining Pokemon left is hoping for the world to not end!
- At first it can be annoying when you get told how to complete certain missions over and over every time you do them. We can get it the first time! Geez, it's like they think you're a child or something. That's when it hit you: They DO think you're (the hero, not the player themselves) a child.
- When the teacher first brings up the subject of evolution in school, the class reacts in general, but the immediate surprise comes from Shelmet. It makes sense, considering a Shelmet's evolutionary process requires two Pokémon, a direct link between them, and the removal of clothing...
- Whenever Archen is in a dispute of some sort, you will usually see him just kinda give up on the topic and let the other side win out as though he's certain he lost already. Now what was Archen's infamous ability again?
- Early in the game, your partner comments that the two of you will make as many friends as there are stars in the sky. The Connection Orb layout has the Pokemon you connected to resemble stars, and the connections between them make them look like constellations.
- When you finally meet Dark Matter, it grouses that it's "you two again". Initially this makes no sense as you've never met Dark Matter face to face before this moment, however, both your partner and you have met Dark Matter before, as Mew and Mew's human companion in the war against Dark Matter in the past.
- Dark Matter thanking the player and partner when you finally end it for good makes a lot more sense when you consider the fact that it literally runs on all negativity, including self-loathing and depression. While it was trying to kill everything, it may have actually been a suicide attempt.
- The reveal that all the main games take place in the same universe means that the Mystery Dungeon world has suffered at least four near-apocalypses in the span of a few years and is undergoing a fifth.
- At the end of the game, when your partner has to leave the world because they absorbed the dark matter, you see your character on their hands and knees, crying that they're gone, not again to be seen by anyone. And the way that your partner words it almost makes it seem like they're, in a way, willingly dying. In a way, you just watched your best friend commit suicide.
- And then there's the whole thing from Carracosta's point of view: One morning after your adoptive child comes home from saving the world and celebrating, they tell you that they saw something cool up on the hill. While they're out, the child learns how important they are to history and that they must disappear from the world, waiting just long enough to tell the player character. Imagine having to break the news...
- What happened to the Pokemon that were Taken for Granite while flying? Did they plummet to the ground and experience Literally Shattered Lives? The also could've fallen into the sea and sunk, meaning they'd be de-petrified... and find themselves on the bottom of the ocean.
- If there's any consolation, the on-screen victims of this Latios and Latias are at least shown to be intact upon crash-landing. Though that's still small consolation for those that fell into the sea instead.
- The anime world is in danger! Think about it for a moment:
- In Pokemon the First Movie, a Pokemon's pure hatred and anger turned someone to stone.
- In Lucario and the Mystery of Mew, a huge tree with a strong connection to Mew is overrun with blob monsters that can mimic the appearance of Pokemon and swallow people whole.
- In Diancie and the Cocoon of Destruction, Yveltal goes on a rampage, turning everyone in its path to stone, and only Xerneas can calm it down.
- How did Yveltal and co manage to turn Wailord and other Water Pokemon in the sea into stone? None of them can breathe underwater.
- Nothing's saying we saw every minion. Maybe Dark Matter possessed some water type Pokémon behind the scenes.