Okay, so this theory revolves around the Law ending of Shin Megami Tensei IV. In this particular ending, Jonathon, You, the Herald Angels, and Tokyo all are annihilated in the name of God. But why? Why, exactly, does God, the being that created everything, good and evil, want to annihilate a city filled with innocent people struggling to survive? While there are demons there, that's not enough to justify the genocide. Many of the demons you encounter are Lawful demons, meaning they fall on God's side. Others are either neutral or fall into the Chaos alignment.
Next, we take a look at bits and pieces of information regarding the Arch-Angels appearing in Tokyo before it was covered by bedrock. Certain NPCs will tell you about a giant cocoon found in Tokyo. According to the NPCs, Angels lived in it, and on occasion, kidnapped children who were "chosen" the create a new world. One over Tokyo. Those left behind in Tokyo were then dubbed "Unclean Ones". People left behind by God.
The only way between the new world and Tokyo was through a dangerous dungeon, filled with demons, which was named Naraku. Naraku led directly to Tokyo's Sky Tower. However, simply getting to the top of the Sky Tower and going through Naraku wasn't enough. You had to get past Medusa, a demon who's gaze would turn you to stone. By the time you arrive to Medusa in Shin Megami Tensei IV, she's already turned well over a dozen people into statues.
While, yes, in the Law Ending, you kill Lucifer, his goal was to destroy Mikado. To destroy the world that God had so desperately tried to make.
In the Messiah ending, you destroy the Universe, saving humanity from itself forever; saving humanity from the wrath of God and Lucifer. It is also not what God wanted done. He wanted Tokyo destroyed. Not the Universe. He wanted Mikado to continue, while no longer worrying about Tokyo's problems. Please note that it is called the Messiah ending. Messiah is usually used in reference to the term savior. As stated before, in this ending, you're the savior and destroyer of humanity. So were you really the destroyer of humanity, as God would put it, or the savior of humanity?
While there are many questions that still need to be answered, I am unfortunately unable to answer them all.