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Nicholas, upon seeing a robot hand as their image for the next world, freaks out thinking that they're in a Terminator-style world. It takes quite a few people to tell him it's just the main character's artificial limb and that they're in a less techy world.
When hailing Tsukasa, Griga performs the Shocker Salute. Complete with...
Wataru and Tsukasa deliver a few during the meeting. The context is that Wataru is King of a group that hates Tsukasa, so he has no choice but to follow their orders, sort of like an Extreme Doormat with a mix of You Can't Fight Fate. Soon, Wataru begins to consider forcing his allies into obeying Tsukasa. To which Tsukasa says...
"And so the balls grow."
And later on, Wataru begins to get an idea from Roy Mustang. That he'd liberate worlds conquered by Tsukasa. The fact that he admits this is his plan right in front of Tsukasa's face is awesome in of itself, and what he says crowns it as both a moment of funny and awesome.
"Watch me. Watch as I grow a pair."
Superpro's constant mangling catchphrases and general idiocy make him a walking one, but one moment in particular stands out. When he bungles an attempt to serve Majora, he intentionally tases himself.
Late in the RPG's run, a second Ciaran came to Gotham and was dropped off by Lewis at the bank where Doomsday was. His response upon finding the Gaoh-Liner was priceless.