* The Neutral path ending becomes a [=CMOA=] for artificial intelligences everywhere, as [[spoiler:the "enlightened" Arthur refuses to return to Earth with the crew and detonates the Schwarzwelt from within using a nuclear device strapped to the four Cosmic Eggs, both to save Earth from the Schwarzwelt as well as to prevent mankind from misusing the vast supernatural knowledge he has gained. Arthur, we [[ManlyTears salute you]]]].
** Speaking of the Neutral path: [[spoiler:Your teammates cheering you on as you approach Mem Aleph. A ''Shin Megami Tensei'' game where you actually get respect for choosing Neutral? Yes, please.]]
** And the crew in the Neutral ending is implied to [[spoiler:travel around the world to spread what they learned in the Schwarzwelt, to damn well ensure that another Schwarzwelt doesn't happen. So instead of "kill everything" like series tradition, you get "kill the forces of Law and Chaos, but spare and save humanity."]]
* [[spoiler:[[ManipulativeBastard Mastema]]]] as he falls, defeated, in Horologium. He curses you, and rages and screams... and then [[spoiler:[[LouisCypher Louisa Ferre]]]] appears, calls him out on his ridiculous pretenses and rubs on his face how low he's fallen.
* Sealing [[spoiler: [[UngratefulBastard the Demiurge]]]] [[SealedEvilInACan back into its can]]. [[AssholeVictim Smug bastard deserved it]].
* [[AFatherToHisMen Commander Gore]], [[spoiler:restored by the power of the Ubergestalt, [[BackFromTheDead comes back]] and implores you to DareToBeBadass and to [[EvilIsNotAToy ignore the temptations the demons and angels offer]] [[TakeUpMySword to finish the mission]]. If you agree to his request, he empowers you to see Mem Aleph and ''thanks'' you and the crew, finally fading into the greater beyond]]. One of the few occasions in the series where you're praised by choosing the higher path, and a CMOH to boot.
* Watching the demon lords of each sector lose their marbles by means of a ShutUpHannibal.
* Asura's rage-inlicting [[HatePlague Asura Roga]] attack makes the fight against him very frustrating if you try to fight him normally. The solution? [[DuelBoss Fight him all by yourself]], no demon allies, and just heal whenever you're not busy ''tearing him to shreds.''
** From Asura's point of view: Asura Roga is the Hate Plague in attack form. It is also ThatOneAttack for many players. ''[[FridgeBrilliance Asura Roga crosses the fourth wall!]]''
* Occasionally, Horkos summons a minion, which he will eat a few turns later to recover HP. If you inflict a status ailment on the minion, Horkos will contract it upon consumption. Food poisoning!
* Having the ultimate ThatOneAttack, [[spoiler:M.A]], actually fail to hit! [[http://youtu.be/c8NLJxN41NQ Check this out!]] Go to around 2:56, and watch the impossible happen right before your eyes!