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  • Alternative Character Interpretation: Some fans theorize that Aleph killing YHVH in the Law route is meant to symbolize the New Testament overcoming the Old Testament given that the former is a Clone Jesus while the latter is based off God's more Jewish portrayal. The fact that Aleph in his appearance in a DLC for Shin Megami Tensei IV: Apocalypse as a representative of the Law route adds fuel to the fire.
  • Anticlimax Boss:
    • The Twelve Shinshou. They are mentioned as early as during the first trip to the Abyss, and you start to mentally prepare for an epic Boss Bonanza that requires careful conservation of resources... only to find out that they're complete pushovers who die in 1-4 turns, have trouble consistently hitting your party and yield less XP than a Random Encounter.
    • Kuzuryuu is very important to both sides' plans and is the only Neutral exclusive boss in the game. He ends up being relatively easy compared to Lucifer beforehand and the Shinreis afterwards.
  • Anvilicious: The subplot about the poor Woobie Shinto gods being imprisoned by YHVH so no one can worship them anymore is about as subtle as a sledgehammer upside the head. It's a pretty strange anvil to drop, considering that the Shinto religion has always been exclusive to Japan and the number of Christians in Japan is less than one percent of the population even today. (Having Amaterasu Herself go on a bit of a tear about "grasping Hebrew Gods" gets a bit uncomfortable, to boot.) It then gets even weirder with the Raidou Kuzunoha games revealing that the Amatsu once sided with YHVH to persecute the Kunitsu.
  • Ass Pull: Satan betraying YHVH in the Law route can come of as pretty much out of nowhere with no foreshadowing for it happening. In later releases with the Visionary Items they tend to avoid this, having a specific one that foreshadows Zayin turning on YHVH because God's Judge is meant to judge everyone, no exceptions.
  • Broken Base:
  • Complete Monster:
    • The twisted versions of Archangels Uriel, Raphael, and Michael are overlords of the theocratic dictatorship that has overthrown Tokyo After the End. While they allegedly divided the city into five districts in accordance to the division of labor, it is clear they favor the wealthy Central District and feel free to neglect, abuse, and slaughter outright the residents of the other four. When signs of rebellion appear in the Valhalla district, they order the Demon Lord Abaddon to devour it whole, promising to restore his angelic status if he did so; when he is finished, they cast him back into the demon world. The entirety of the Arcadia district has been lobotomized and plugged into Lotus Eater Machines, causing them to believe they live in an idyllic paradise while their physical bodies waste away; Aleph is subsequently informed the the Archangels intended to do the same to the entire planet. The workers of the Factory District have been brainwashed into slavery by the song of a Siren, who is routinely tortured by the Archangels' henchmen to keep her singing. Finally, they attempt to get Aleph and his comrade Zayin to surrender to them by holding the entire Holytown district hostage, threatening to cut off their air supply and slowly suffocate them to death.
    • The Center Bishop, as revealed by the Visionary Items in the remakes, is the Archangels' top enforcer. As leader of the Temple Knights, the Bishop orders the execution of all captured rebels, even killing children without offering them a second chance. Also overseeing the Messiah Project, the Bishop provides Mekata with a supply of infants to test his rapid aging procedure on; when Mekata protests that the Bishop's requests could kill them, the Bishop responds that he'll keep providing Mekata with babies to replace the dead ones and to put it out of his mind. Also in charge of the education of the children born from the project, the Bishop ensures their only desire is to follow their assigned role, taking a particularly sadistic delight in tricking Daleth into believing he's the Messiah. When Aleph resurfaces, the Bishop turns a Jack Frost into King Frost and lets him ravage Holytown, but leaves out his true role as a sacrifice for the Messiah's rise to power.
    • YHVH. See that page for details.
  • Crosses the Line Twice: Yes, Mara appears, but he doesn't have the Hurricane of Puns surrounding him this time. No, this game has Crowley/Master Therion, who holds Sabbaths to have sex with demons and, when forbidden to by Lucifer, complains about how horny he is and decides to kill you to calm himself.
  • Ensemble Dark Horse:
    • This is the game that introduced Alice as an enemy. Also, while he didn't gain his popularity until the next game, this is also the game that introduced Matador.
    • This game's alignment representatives are Zayin/Satan and Lucifer. They happen to be among the most popular alignment representatives due to Zayin managing to defy the initial Lawful group and hold onto himself as he sinks deeper into Law and even managing to turn on YHVH in the Law ending, which most Law heroes either never do or only realize as they die, and this incarnation of Lucifer being a Well-Intentioned Extremist leaning heavily on the Well Intentioned side, to the point where it's this Lucifer most fans generally default to.
    • One of the many Messian types you can fight in this game are the Terminators, who are based on exactly what you'd expect. Despite only appearing in this game, they're far and away the most popular regular enemies in the game, with many clamoring for them to return in some form.
  • Even Better Sequel: While the first game is nothing short of groundbreaking for its time, this was the game to introduce many of the most interesting concepts to the series and features one hell of a weird, interesting and surprisingly deep story for a Super Famicom game. In addition, this is the first time the series introduced Lucifer and YHVH, both of whom would go on to develop the ideological conflict between Chaos and Law to a much more interesting angle.
  • Game-Breaker - No, not Zio. This time around it's damage and defense buffs and debuffs, which stack with themselves and last until they are dispelled, something that not every boss is capable of. But more-so is the Divine Retribution spell. It tears off a quarter of an enemy's health with an alignment opposite to the spell's caster, and it works on bosses with no reduction.
  • Hilarious in Hindsight:
    • The Puck subquest, in which Daleth tries to screw you over with Infidelily Sap, and how it comedically backfires is funny by itself. However, when the reveal about Hiroko being Aleph's mom is discovered, it gets more hilarious when you realize Daleth got your MOTHER to chase him around like a lovestruck twit!
    • As mentioned under Memetic Mutation below, fans compare YHVH's appearance to a yellow-skinned Jean-Luc Picard. Come Shin Megami Tensei IV: Apocalypse, YHVH is voiced by Mugihito, who voiced Picard in Star Trek: The Next Generation's Japanese dub.
  • It Was His Sled:
    • God (as in capital-G God) being the Big Bad and the Final Boss on all three routes is one of the most well-known twists of not only the game, but of the entire franchise.
    • For those who know more about the game's plot than the above entry, Zayin being the human half of Satan is also very well known.
  • Mainstream Obscurity: Most people with even a cursory knowledge of Shin Megami Tensei know this is the game where you fight YHVH. The number of people who know anything else about the story, let alone have actually played the game, is far smaller.
  • Magnificent Bastard:
    • Lucifer returns, see his original game's page for details.
    • Zayin was created artificially as part of the Project Messiah in order to be the Messiah's bodyguard, but his destiny was to be much more. Introduced as a loyal Temple Knight working for the Center, capital of the totalitarian and hypocritical Tokyo Millennium, Zayin eventually discovered their murderous corruption thanks to his time with Aleph and decided to rebel against it, broadcasting the truth and gaining a loyal following in the religious district of Holytown. Forced by The Elders—actually corrupt archangels—into going to the Center after they threatened Holytown, Zayin is captured and then freed after Aleph defeats them. Building a new Eden—filled with people whose "knowledge" was erased—alongside the archangel Gabriel, Zayin is revealed to be actually a part of Satan, God's instrument to judge all creatures. Embracing his role, Satan prepares to destroy both the human and demon worlds, leaving only the peaceful people of Eden to build the Millennium Kingdom, managing to doing it in the Law route before ending his judgement by judging his creator, God Himself. Having finished his holy duty, Satan leaves the future to Aleph and Hiroko before returning to the soil from where he was created.
  • Memetic Badass: Aleph is generally put in the top tier of SMT protagonists along with the Demi-fiend and Nanashi. This most likely has to do with how the endgame of Neutral pits him against Lucifer, the giant dragon Kuzuryu, three avatars of YHVH, Satan, and YHVH Himself.
  • Memetic Mutation:
    • "Everyone's dancing furiously."
    • A number of fans have pointed out that YHVH looks like Jean-Luc Picard with yellow skin.
  • Moral Event Horizon: See here.
  • Narm: If you refuse to side with Zayin and Gabriel, they will throw you out of Eden, telling you that you are Beyond Redemption. However, the sound effect that plays during this moment and the way you land outside the Center's entrance without any harm done seem to imply that they literally just picked you up and tossed you out the window.
  • Nightmare Fuel
    • Valhalla is swallowed by Abaddon. Whose stomach is a dimensional rift. You get to explore his fleshy insides, culminating with a duel against his heart.
    • If you strongly believe in an Abrahamic religion, have fun trying to complete the game. Because at the end of the game is a twisted version of God as the Final Boss. Unlike in SMT I, where following Law means you side with him, in this game you still fight him, and just to drive home how terrible he is, even His angels want him gone.
      • Frankly, YHVH is pretty creepy even if you don't believe in him, as He's smack dab in the middle of the Uncanny Valley, giving you a perpetual Death Glare, and begins the fight with a rant about how you deserve to be tortured for all eternity (said tortures described in excruciating detail) for daring to be the good guy here. Oh, and if you're playing on certain emulators, the dialogue box constantly shakes.
    • If you followed the Law Route, you essentially support the eradication of all life on Earth. If you chose to destroy the Arcadia System Gimmel is in control of (Chaos), everyone hooked up to it dies, it's even worse if you take Gimmel's place by inputting your data (Law) since everyone who is hooked up to the System would die anyway cursing Aleph for letting them die.
  • One-Scene Wonder: Crowley and YHVH, the former for his out of nowhere hilarity (I'M SO FREAKING HORNY!) and the latter for what He does as the Final Boss and Big Bad, even on the Law route.
  • Player Punch:
    • The intro is this for those who beat SMT I on Neutral. Oh, you thought that paradise of balance was gonna work out? Well guess what, that didn't work, and now humanity is cooped up in a domed metropolis run by horrible religious fanatics with the rest of the world uninhabitable by humans.
    • The fact that the corpse of the Hero from SMT I was found in the backstory as having died alone in a cave-in, again for those who have played the previous game. You already knew this person's plans didn't work out, but to see that he died alone in a cave? Damn.
  • Scrappy Mechanic:
    • Partway through the game, the Center becomes off-limits, and naturally the Terminal stops working as well. Later in the game, you get access to the Center again, but the Terminal's teleport function never reactivates. The nearest Terminals all require a good few minutes of walking to get back to the Center, resulting in a good deal of padding whenever the game expects you to go back to the Center.
    • At various points in the game Aleph will be checked for a particular stat in order to proceed, requiring either intense Level Grinding or incense consumption in order to pass the check. The worst of these are any stat check that requires Magic, as it does nothing to help Aleph due to him being a purely physical fighter. You can at the very least cheat the system for the plot-mandatory checks by giving Aleph stat boosting equipment and drinks from the Bar, but the Kongokai checks circumvent those bonuses and only search Aleph's pure statline.
  • Signature Scene: The battle with YHVH is one of the most remembered parts of the entire franchise. While it's the least liked route, Law's version of it is probably the most well known, as Satan realizes the gravity of what just happened and calls YHVH out, proclaiming that it's time for the ultimate creator to be judged.
  • That One Attack: The last two bosses of the Neutral and Chaos routes and the Final Boss of the Law Route both have one hit kills they can use any time. Granted, they do use it on specific targets, but it's still extremely annoying.
  • They Wasted a Perfectly Good Plot: The Archangels' twisted view of YHVH willing a fake one into existence feels a bit pointless once it turns out the real YHVH is exactly as evil as the fake.

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