- In one of the Fortress of Solitude raids, Krypto is mind-controlled by Brainiac to attack. When the control is broken and Brainiac's forces are defeated, Lex calls it an "insane mutt" but Superman retorts that "maybe one day you will understand loyalty, human or animal".
- The Booster Gold exploration tours are full of jokes and grandstanding on Booster's behalf, all spoken in a very cheerful and cocky manner. When he gets to Leslie Thompkin's free clinic in Gotham, however, he speaks very seriously and sullenly out of respect for the clinic, noting that "This Booster Gold endorsement is provided free of charge".
- Near the Crime Alley kiosk in Gotham you can visit the spot where Bruce Wayne's parents were murdered. There laying on the ground is a bouquet of roses undoubtedly left by their son.
- In some of the higher leveled villain quests, Calculator seems to be more genuine in rooting for you and/or wishing you success.
- This troper recently found that you can stop certain citizens from committing suicide. Let that sink in for a second.
- A villainous example with Black Adam, who vows revenge against you after you destroy a revived Isis. Came Back Wrong be damned.
- After saving Smallville, Martian Manhunter thanks you and your team, saying that "it means more to some than you know."
- Beast Boy's line in the Gotham Wastelands
Trigon's sons think they're Raven's family. They're wrong. We are!
- In certain Raids, if you're knocked out, there's a chance you may be revived by any NPC allies you have fighting alongside you, which is heartwarming enough, but depending on the Raid, you may even have Villain NPC allies reviving you when you're down, a good example is during the fight against Brainiac in one of of Fortress of Solitude Raids where you might get revived by Lex Luthor or even General Zod, showing that even the the foes you usually fight against recognize an Enemy Mine situation and signifying the fact that whether you're a hero or a villian, you're ALL fighting to protect Earth from the same threat.
- In the Phantom Zone alert, the player team is trapped in the Phantom Zone due to a trap meant for Superman, and weeks pass outside until the latter rescues them, and he said a certain reporter has saved the newspapers if they need to catch up.
- After completing the Mirror Image: Justice League briefings, Superman sends you this message, reminding you that yes, you are a part of the Justice League:
The Justice Legaue historical files on this other Earth are invaluable. Looking forwards to hearing yours when you make one.