- The place where Maddison Hayes' final "boss battle" was fought was called Coeur Tower. As in Core Tower.
- The three original leaders of Team Liberty also got their codenames from the Guard Teams in Digimon World 2—Gold Hawks, Blue Falcons, and Black Swords (with "Swords" being replaced with "Skull" in Blackskull's case.)
- Both Sleight and Meghan Vert have ordered their Pokémon using the phrase, "Would you kindly x?".
- Koga's execution of Nemo Buck was deliberately modeled after the plot-relevant assassinations in Assassin's Creed.
- During a training battle between Ray and Sonja, Ray's Dewott used a spinning Aqua Jet attack written in such a way as to invoke the 3D Maneuver Gear from Attack on Titan.
- Ho-Oh's regeneration ability was based off of those of The Doctor.
- On a similar note, a mysterious and slightly grumpy Doctor and his companion Clara treated both Alex Zyther and Amelia Zann's Carvanha "Van"; during the "Summer Wars" arc in Celadon City, the pair vanished into thin air, though Zann's Larvitar Harvey heard a "strange (mechanical) whine like nothing in the world he had ever heard of" shortly after said disappearance.
- Sheik's nickname came from The Legend of Zelda.
- Similarly, with Ariadne's.
- The description, "Dark-haired, fire-based Badass Baritone In A Nice Suit, Father to His Men military man" could easily apply to either Shadow Admin Sleight or Roy Mustang, although Word of God says that this was unintentional.
- Lafoyae Belrose and Jackson Sang are direct shout outs to Baccano!, which also inspired the initial stages of the story arc that they were introduced in.
- Gold consistently referred to Ray as Ichigo during the Unova Arc, due to the characters' similar appearances.
- While investigating the situation in the Celadon Department Store, Ethan orders the group to "Split up. Look for clues."
- Wrath's last words were a direct shout-out to Lust's from Fullmetal Alchemist.
- Three of Team Zephyr's members have been crafted as expies or blatant references, purely for the sake of comedy.
- Skyler's mannerisms and appearance are a straight-up expy of Shaggy Rogers, complete with a team consisting of a Houndoom named Scooby-Doom, an Ursaring named Teddy Jones, a Klingklang named Velma Klinkly, and a Swanna named Daphne Duck.
- Skylark is obsessed with music, has a brother named Chip, and is part of a band with said brother called the Chipped Skylarks.
- Skye's Pokémon are all named after superheroes. So far she's obtained The Human Torchic, Spinarak-Man, and Zubatman.
- Soil Colossus, Inc.'s entire organization was one big shout out to Smogon's CAP project Collossoil.
- The introduction of the Pokémon Rangers to Sootopolis, showing them descending toward the city from helicopters on the backs of their Flying-Type Pokémon, was a direct reference to the Volume 2 opening from RWBY
- Quentin Dallas's appearance is also directly based off of Roman Torchwick's. Their mannerisms aren't far off from one another, either.
- James and Guinevere apparently once lived in the same orphanage as the Blues Brothers, if Celadon is actually Chicago.
- Alma Mason is a general shoutout to survival horror games' love of creepy children, but she was named after two characters from such franchises. Her first name is a shoutout to the character in FEAR, while she shares her last name with the protagonists of the Silent Hill games.
Shout Out / Pokémon: Rise of the Rockets