For me it's the 3ds games (triple deluxe and planet robobot)
Triple deluxe is just tragic. Especially in the aftermath. Taranza becomes lonely after you kill sectonia, and when you fight Sectonia's soul, the Japanese pause description is told through her perspective where she begs you to kill her. At least, I think that's the case.
Planet robobot... Well, lets just say it's dark. The bad guy has a sad backstory where he thinks he will never bring his daughter back. And when she did return, he barely recognized her. In the (luckily non-canon) star dream soul OS fight, the poor man's soul gets destroyed by star dream. And lets not get started with mecha knight...
Overall, I think robobot is a bit darker than triple deluxe.