Complete Monster: Emperor Nicholas the Puissant, who has conquered the world in an alternate dimension. He kills people who fail him, tortures Nega-Ki to ensure his counterpart's obedience, then threatens to torture prisoners to death in front of him if he wastes time, and it is ultimately revealed that he doesn't want Project Velociraptor so that he can win the war with the aliens laying waste to Earth, but so he can escape and re-establish himself elsewhere.
Rape Is a Special Kind of Evil - Nega-Nick's repeated attempts to get Ki in bed are thwarted each time almost like Ki had Plot Armor or the author saying "No, I'm not going to have that happen". Given that there are several Reality Warper characters on the good guy squad, this is possibly deliberate.
After Fooker leaves to work with the UGA abroad after his cover is blown, his friends look over his belongings, and think to themselves how much they miss him.
Schedule Slip: Hit the comic hard during To Thine Own Self as Jeffrey dealt with medical issues with his firstborn child. What should've been a year-long story arc ended up taking two-and-a-half years, and even then was still curtailed significantly.