(longer, more involved theory-crafting under the cut)
I WAS RIGHT he WAS meant to protect mikoto!!! and the fact that he calls himself the "newborn other you" supports my theory that he's new, probably forming either right before or right after the murder.
"I don't even know the reason why I'm here" and "[He's a liar,] you said, and made me out to be a scoundrel, why?" sounds a lot like even Niko doesn't fully remember what happened. Also, I looked into the lyrics (as I do), and I found some interesting bits in that second line. Take this with a grain of salt, I'm not a native Japanese speaker, but I did my best to look at resources from fluent speakers (like Japanese dictionaries) to explain nuances.
I find it interesting that they chose to translate 悪者 (warumono) as "scoundrel", rather than something else. Literally, it means "bad guy" (warui = bad, mono = someone/person), and thus could be translated a number of ways. Villain, bad guy, ruffian, rascal, etc. So why scoundrel? Is it another case of strange translation, or does it mean something about Niko?
Also....considering how clear the first MV was with 1) WHERE the murder happened, as well as 2) the Kotos whacking an Actual Human Person, I strongly doubt that the implied Subway Rampage happened here. In fact, the entire thing feels like it's happening while Mikoto is having a mental breakdown and lashing out. None of it feels real, not like MeMe did (at least, the parts taking place outside Mikoto's brain).
I think Mikoto is (or at least was) suffering from the culture of overwork that's common in Japan: karoshi, or "death from overworking". Obviously he's not dead, but he definitely wasn't looking so hot in that MV. Eyebags, dark circles, exhausted posture, and bedraggled appearance were just a few things I picked up on my first run-through. His clothes, while fashionable, are loose, baggy, and cover his body completely. For someone like Mikoto, who's so meticulous about how he appears to others, to purposely dress like this? It contrasts so much with his flashy hair and piercings that one has to wonder why?
It's a ruse. Just like how peacocks have false eyes on their tails to deter predators, I think Mikoto's flashiness is meant to draw attention away from everything else. Any inconsistencies can be explained away with a makeup mishap (because you can't tell me this man doesn't wear foundation and concealer at a minimum), and having stylish clothes distracts from how otherwise baggy they are. Baggy clothes in themselves are a smokescreen, too. They hide your physical form, making it so it's harder to tell the true build of someone underneath.
Kotoko uses this to disguise herself in Harrow, which leads to the police looking for a bulky, middle-aged man instead of a 20 year old female college dropout. Mikoto uses his clothes differently, meant to distract from anything "concerning" about him that can't be brushed away with a laugh or a smile. I think he's trying to hide being too thin or malnourished, since stress and overwork can lead to fatigue, poor nutrition, and a host of skin problems. Hiding that behind baggy clothes and a layer of makeup means his ditz mask works better, and anyone sharp enough to look past it....well. I'm not actually sure he's met anyone like that, if his phone call with his mother was any indication.
The point is, I'm worried about him. I think his murder was a result of a mental breakdown but not, as I thought earlier, from anger, but from stress. Stress from overwork that led him to the point of death, and it was just bad luck that meant it was someone else's rather than his own.
Again, this is all just a theory, and I haven't listened to the VD yet. But I will say this; I've been there, and while I haven't killed anyone over it there were times I got damn close. I may not agree with him, but I understand, especially if he has nobody who knows the Real Him. I was lucky enough to be able to vent to my friends about my job and school before my stress breakdown consumed me, but I don't think he has anyone like that.