* The ending, [[spoiler:in which we see the reincarnated Embryon (and Angel) playing in a field under the care of the now-adult Fred.]]
** [[spoiler:Everyone rising with Seraph to reach The Sun, including Madame, Angel and Roland.]]
** The state of Earth at the end of the game. [[spoiler:From what little we see, it's in really good shape, and there's no sign of anything bad happening in the future. Given that every other entry in the franchise, even ''Persona'', has something bad with the world at the end, whether through the ending itself, the threat of the villain coming back or a new one, or knowing that there will be another game in the same world released later, this game ends with a very nice breather that makes you feel like your efforts really were worth it]].
* Just before the fight against Mick the Slug, when Bat tries to tempt Heat away from the Embryon, Heat turns on Serph and attacks, forcing you to choose whether you're willing to fight him seriously or say that "You can't"... only for Heat to whisper, "Play along!" and let others use the "fight" as a distraction - cementing that for all he is TheRival, Heat is still Serph's loyal right hand and that showing your trust in him truly pays off.
** Later, when discussing how the YouKillItYouBoughtIt laws of tribal loyalty are breaking down, Heat bluntly declares that if someone else killed Serph, he'd just take over the Embryon himself rather than join another tribe. The others agree, placing their friendships and their loyalty to the tribe over the Karma Temple's laws.
* Yu Godai's alternative telling of the series in the novel ''Quantum Devil Saga''. Just in Volume 1, [[spoiler: though the Embryon has to use Sera's blood to calm down rather than song, Cielo gets a CrowningMomentOfAwesome by shoving Sera in a gun locker and single-handedly holding the room from the Solids, even losing an arm in the process, Jinana survives her berserk state and calms down, Bat and Mick are forced into imprisonment by the Brutes and Sera elects to learn how to use a gun to defend herself.]] ''Optimism''? In ''my'' Shin Megami Tensei spinoff?!