- Look at how the Pikachu in this trailer looks at himself (paws, then ears, then underneath itself, then its tail) and compare it to how Alesia looks at herself when she first discovers she's an Eevee.
- Ambient Cave having Golbat inside is a nod to the swarm of Golbat in Sinister Cave from the first anime special.
Alesia Versus the Law
- The Kecleon brothers and Kangaskhan were the only Pokémon from Pokémon Square in Rescue Team who retained their roles in Treasure Town in Explorers, while all other shops were run by different Pokémon. The Kecleon brothers and the Kangaskhan in Izolo Village are also the only shopkeepers to be recycled from the previous games.
- Alesia's (mental) line "Really wasn't expecting this sort of welcome..." is lifted directly from the second anime special when Piplup and Chimchar are confronted by the members of the Wigglytuff Guild.
A Mutual Cause
- Alesia's Joy Ribbon is off-white with cyan polka dots, and the EXP bar in the core series games is off-white with cyan rectangles indicating the amount of experience points. Riolu's Power Band is vermilion with a horizontally-stretched yellow eight-point star, the same as the Physical icon in the core series games. Popplio's Special Band is purple with three lavender rings, the same as the Special icon in the core series games.
- The Purple Kecleon being missing while the Green Kecleon is still in Izolo Village is a nod to how the Purple Kecleon was absent from Gates and Super, with only the Green Kecleon running those games' shops.
- Alesia's dream has her floating through an "ethereal dimension of continually-fading out and in colors" with a strip of "white light in sharply-zigzagging directions", a description that matches the dimension the personality tests in Rescue Team and Explorers (and the dream sequences in the former) take place in.
Digging for Truth
- Kangaskhan letting Team Everlasting borrow pickaxes and hardhats for their journey into Marble Cavern mirrors the first anime special where that Kangaskhan gives Team Go-Getters Pecha Scarves (to keep).
Climbing the Ranks
- Popplio gives Alesia a score of 8.7 after she crosses a river. IGN would like to have a word with the author...
- Prior to the chapter, Popplio once suggested calling his and Riolu's future team "Riolu's Enforcers", but they decided not to because it featured only one of their names, lacked alliteration, and would have been awkward to fit on the back of a badge. The second criticism isn't applicable to the name Emolga suggests Emolga's Enforcers in Gates To Infinity, but the third is.
- Riolu thinks of Alesia as "the sort of Pokémon who would feign having a stomachache from spoiled breakfast in order to get out of entering a scary dungeon". Bringing back any humorous memories of the partner from Rescue Team?
Riolu in the Tyrunt's Den
- Riolu's patient number in Blissey Medic is 447, which corresponds to the species' Pokédex number in the main series.
- The friends Popplio meets in his dreams are a Rowlet and a Litten. This goes without explaining.
In a Rich 'Mon's World
- The Aurorus that Team Everlasting have to deliver a package to has Vigoroth and Machoke employees working for him. While Pokémon Ruby and Sapphire starts out with Machoke workers helping with the player character and his/her mother's house move, Emerald replaces them with Vigoroth.
So Proud and So Brave
- Golden Tickets are referred to in this version as simply Gold Tickets, something you can trade unwanted items for in Spinda's Cafe.
- The contract in this version is hidden not behind curtains, but on the other side of the wall, and panels flip over to show it, just like the job board in Explorers when Dugtrio and Diglett have updated it.
- "Hold your breath. Make a wish. Count to three. Smiles go for miles."
- One not for the Pokémon Mystery Dungeon series, but for the original novel: the line "the time was ripe to send her shooting up the pipe" is only slightly changed from a line in Augustus Gloop's poem (which was made into a song in the 2005 movie).
- The Plazania (a boat made in the likeness of a Piplup) is actually one of the boats in the Wi-Fi Plaza in Generation IV.
- Another one for the original novel: when his four companions have all been eliminated, Popplio is afraid to continue because he doesn't want to "get cut into squares or burst with heat or get ground into powder". These are all fates that threaten to befall some of the children in unused drafts for the novel.