- Actor Allusion:
- Gabriel isn't the first time one of Dave Fennoy's characters contracts a deadly infection because of a major antagonistic force, depending on your choices.
- Roger L. Jackson, in Episode 6, plays a murderer who wears all-black clothing aside from a white mask, with the voice being used to hide the identity of the person under the mask, similar to Ghostface.
- In Episode 8,Hadrian uses the phrase "Ta Ta for now", reference to Jim Cummings role as Tigger.
- If Jesse chooses to accompany Lukas and Radar in Season 2 episode 2, they will be forced to run from Snow Golems. Radar is afraid to jump a large gap and Jesse responds with "Sometimes you've just got to fake it, Radar. Hero time!"
- Ascended Fanon:
- The characters and animation style in the game look very similar to popular Minecraft animations, with the characters having a similar range of expression (but their faces move slightly differently in this game, looking more "stop-motion") and bendable limbs.
- Sky City is based on the popular SkyBlock game mode commonly found on multiplayer servers, including the cobblestone generator most players usually build first.
- Casting Gag: Throughout Episode 6, Dan's hair changes randomly, with a couple characters commenting on it. This is a reference to Dan changing his hair color regularly IRL, and modifying his Minecraft avatar accordingly when that happens. In addition, if he's the one who dies third(only possible if Stampy is accused of being the White Pumpkin), then his inventory will include what appears to be an actual Diamond Minecart.
- Celebrity Cameo: One of the stranger instances of this happening. Episode 6 of Story Mode features several YouTubers, as well as original characters TorqueDawg and CassieRose. However, in an odd coincidence, there actually IS a YouTuber, albeit a low-key Toon Town YouTuber, with the username of "Cassie Rose", whose subscriber count has doubled since the episode came out. And she is finding this situation to be REALLY weird.
- Cowboy BeBop at His Computer: In-game. In Season 1 Episode 4, you come across some Prismarine Shards which are labeled as such, but when you click on them, the dialog calls them Prismarine Crystals. Doubly glaring since Season 2 features both Shards and Crystals and correctly identifies which is which.
- Development Gag: The Order of the Stone is actually an old subtitle for what would become Minecraft, with the full title being "Minecraft: Order of the Stone".
- Fandom Nod:
- Some of the Redstone machines in Redstonia have actually been created in Minecraft proper, like the Redstone flying machine and mech.
- The Wither Storm's weakness brings to mind a popular player tactic that fairly easily nets a Nether Star. Swarms of Endermen weaken the Wither Storm, much like how Withers, when spawned in the End, are outnumbered by Endermen, who can make very short work of it.
- Episode 7's PAMA is likely a nod to those who have successfully built redstone computers in Minecraft.
- Episode 8 features Spleef, a favored minigame of Minecraft players.
- Playing Against Type:
- Post-Script Season: Episodes 5-8 are this to the Wither Storm crisis. To wit: Jesse and their new Order of The Stone have spent an indeterminate amount of time after the death of the Wither Storm and Rueben, going on adventures. One of those adventures gives them an enchanted flint and steel, which opens a portal to a new world. After resolving the new world's issues, they suddenly find a large hall full of new portals and new worlds.
- Promoted Fanboy: Episode 6 has several prominent Youtube-based Let's Players that specialize in Minecraft content as crucial characters.
- Viral Marketing: The antagonist of "Access Denied", PAMA, has a Twitter account that promoted the episode before its trailer went up, and hinted at his overall goals.
- What Could Have Been:
- Lukas had an entirely different design in the original trailer, wearing a striped shirt, vest, and a Nice Hat. He also seems to be with the group from the beginning, as opposed to part of the Ocelots.
- Magnus's title was "Griefer" at a certain point rather than "Rogue", the change being presumably to fit into the naming convention of The Order of The Stone, as he's still identified as a Griefer when you meet him.
- The first trailer showed Otis the Butcher and the Ocelots getting ready to enter the Nether Portal with Jesse's gang, indicating that they may have been intended to play a larger role in the Wither Storm arc.
- A lot more was supposed to happen is Season 2, but got cut due to budget restrictions or other reasons. Em would've appeared if you chose to convince her to come back with you, DanTDM or Lizzie would've appeared depending on who survived "A Portal to Mystery", and Lukas may have not been absent from Episodes 3 and 4 if not for his voice actor becoming a father at that time. Also, they were hoping to do a flashback sequence featuring Romeo, Fred and Xara, all in their Admin forms.
Trivia / Minecraft: Story Mode