Plenty of spoilers for recent chapters ahead, read with caution!
- Metal Gear: The first major story arc of the story is a love letter to Metal Gear
- In the prologue, the characters of Kaz Mizusawa and Fantomu Payne both initially reference the Konami franchise in both name and mannerisms. Later, Kaz actually becomes the first major antagonistic character the protagonists must face in their return to the Metaverse. His cognition has been altered to view his office as a military base, and the entire "Fort Kaz" story arc becomes an exercise in stealth sneaking and gun fighting action in the spirit of Metal Gear.
- The larger conflict of this arc is the threat of an experimental prototype of a bipedal nuclear armed mech named the Icarus, which is an homage to Metal Gear REX. The Icarus even appears to have the same weakness of being blind without the help of a radar dome device, just like REX was.
- A special verbal code that the Phantom Thieves are told to speak to a future ally is a reference to an obscure quote from the first Metal Gear. "The story started to move" is a callback to the line "I goofed! The lorry started to move," which Solid Snake says before being mistakenly driven to a different location after sneaking into the back of a military truck.
- Devil Summoner: As the Ace Attorney characters delve into the Metaverse for the first time, Phoenix Wright finds himself in a unique situation. His personality and attorney mentality of helping others seem to manifest in a way that puts him in a position of a Devil Summoner, rather than a Persona user. This is in homage to the Shin Megami Tensei origins of the Persona series.
- Music from the Devil Summoner series of games have accompanied various scenes in chapters from Phoenix's perspective to further this comparison.
- The first Shadow that Phoenix forms a partnership with, Minamoto no Yorimitsu, actually goes by the nickname of "Raikou." This is not only authentic to the actual Japanese folklore figure that Raikou is based on. It is also meant to reference and evoke the name of Raidou Kuzunoha of Raidou Kuzunoha vs. The Soulless Army fame.
- Some Chapter titles are self-referential to Ace Attorney or Persona 5.
- 1-3 — "Following the Meta" refers to gaming terminology where players will define something (a character, weapon, strategy, etc) as "meta" when it is generally agreed to be the most efficient or effective way to play a game, but more importantly alludes to the currently unknown state of the Metaverse that the Phantom Thieves are trying to investigate.
- 2-2 — "Dueling Destinies" describes the two crossing parties of Ace Attorney characters and Persona 5 characters working towards the same goal in different ways, but is also a joke on the title of the fifth Ace Attorney game, "Dual Destinies."
- 6-1 — "Wake Up, Get Up, Turnabout There!" in general is a pun on the main theme of Persona 5 "Wake Up, Get Up, Get Out There," mixed with the ever-present term "turnabout" which appears in virtually every case title in Ace Attorney.
- 11-1 — "Máodùn (矛盾) - The Word Meaning, 'Contradiction'" is a reference to the trial "Rise from the Ashes" from the first Ace Attorney game. In that trial, Miles Edgeworth recounts the origin of that word based on a folk legend from China. In Logic and Trickster, he directly summarizes the same story while in battle, which not only gives insight to his philosophy but also subtly justifies how his Metaverse weapon manifests as an "invincible spear" like in the story.
- Other chapter titles are nods to other media that the writer is fond of.
- 1-2 — "Invitation of a Crazed Room" describes the state of the Velvet Room, but is a reference to "Inviation of a Crazed Moon," the title of a song from Castlevania: Portrait of Ruin.
- 3-1 — "Brave and Brazen" is a parody of "Bold and Brash," the name of a piece of art that the character Squidward painted in a classic episode of Spongebob Squarepants.
- 10-1 — "Keys to the Ruin" refers to not only the tickets and keys that Phoenix and Maya are given, as well as the "ruin" described in Persona 5 as the ambiguous doom that will come to be if not stopped, but is the title of a song from Sonic Adventure 2.
