- This game delves into what happened as a result of Shin Megami Tensei I's protagonist and his sidekick pursuing a neutral/balanced path where Law and Chaos can coexist. First off, this plan backfired, the end result being an even more Crapsack World where the last bastion of humanity is a domed city where Tokyo once stood, run by Messian fanatics, with the outside world being uninhabitable and infested by demons. And then you can find the body of said protagonist, alone and unburied in a cave. For those who played the Neutral route of SMT I, it feels as if you braved that route (which, by the way, involves fighting bosses from both sides, not just one) for nothing.
- The first real moment is the death of Beth, who blocks Daleth's ultimate attack right before the final phase of his first fight. If you try to kill him, she begs you not to and ultimately succeeds before succumbing to her wounds. You meet her again later with the spirits of the Shin Megami Tensei I characters and Red Bear, where she gives you the last of her power.
- Mekata's death, just after he reveals that the main human characters save Hiroko were his creations and that Hiroko is his daughter and Aleph's mother.
- The deaths of the alignment representatives:
- On Chaos and Neutral, Zayin is completely gone. Satan, who has completely taken over, asks what you will do now that you killed God's judge before dying.
- On Neutral, Lucifer begs you to protect demons and humanity from YHVH, telling you to stop Kuzuryu and Satan before one of them destroys everything. He bitterly laments the cycle YHVH has trapped the world in, noting the endlessness of it.
- On Law...OK, it's not just the alignment representatives. Everything about the Law route is heartrending. When Lucifer dies, he calls the three of you out, specifically warning Aleph that everything is his fault. The three head to Eden, where Satan nukes the world. Realizing what he did, Satan regains his humanity, takes Aleph and Hiroko, and makes one last stand against YHVH, who promises to eternally torture Satan. After they kill Him, Gabriel appears. She talks about how she's lost her purpose and leaves. Satan reveals soon after that he is dying as a result of the battle and entrusts the future to Aleph and Hiroko. They decide to rebuild society in Zayin's name as the credits roll.
- All four of the actual main characters go through a lot in the game. Aleph develops amnesia, is used by the insane Archangels, learns that his main companion is his mother, and is eternally cursed by YHVH to a Fate Worse Than Death - and if Nocturne is anything to go buy, it happens. Hiroko loses her father to Abaddon and deals with her whole life being a lie. Zayin also deals with his life being a lie, but depending on Aleph's choices, he either loses himself or sacrifices himself to defeat YHVH, being the only one of the four to die on all routes. Lucifer was cast into the Abyss for rebelling against YHVH, and dies on two routes, either furious that Aleph and Satan are going to destroy the world or realizing that his battle with the forces of Law will be endless.
Tear Jerker / Shin Megami Tensei II