- The reference-original characters;
- Raindrop - Snowdrop (2013)
- Atlas - The Nostalgia Critic
- Jack - Jacksepticeye
- Aaron and Dan - Game Grumps
- The Ghost Pony - Ghost Pony Rider
- When Midnight declares the Morks to do Operation A113 after invading Twilight's world.
- The Morks' name being a reference to the Gmork.
- When Alternate Atlas comments about Empress Midnight's choice for her new suit design.Atlernate Atlas: Even if you call yourself Batmare, the armour will end up being not intimidating and looking distractingly cute instead.
- Alternate Boris' diary actually mentions Night Lite, Twilight's father from the comics.
- Atlernate Atlas' shout before launching Alternate Daniel from a massive crossbow and Dan's reaction is similar to that of a Brick Joke from Madagascar 3.
- Alternate Daniel's climbing across Mecha Spike, with details sounding reminiscent to Shadow of the Colossus, even to the point of Dan quoting the Game Grumps' Let's Play of it.Alternate Daniel: No, not the shakies, anything but the shaky-shakes,
- The line Mork!Alternate Borris states before colliding into Midnight is similar to what Tron said.Alternate Borris: I fight for Equestria!
- As Pinkie Pie thinks of sequel titles, she thinks of Rise of Empress Midnight 2: Electric Boogaloo.
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