Mainline pokemon WISHES it could tell a story anywhere near as good as this. The game does have it's lows (namely the slow beginning and often repetitive gameplay keep it from being a perfect 5/5 for me), but the highs are so damn high that it has some of the single best moments of any video game I've ever played. Even if you don't care about spoilers for pokemon normally, I suggest you reconsider for this game, as it's got an absolutely exceptional one that I'll get into below.
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So, we all know that moment where we defeat dusknoir, and find out that we're going to disappear if we save the world. But I wanna talk about what comes immediately after that- the scene where our partner is off in the distance getting the ship or whatever ready. Something about that scene felt weird to me at first, but I couldn't quite put a finger on it, then it dawned on me- I wasn't used to seeing the partner character alone. In fact, throughout the whole course of the game, from when the player first meets the partner up until this point in the game, there has NEVER been a scene with the partner in it where you aren't by their side. And that makes sense- you're directly involved in their growth as a character, being the reason that they learn to be confident and brave, and to better themself. So having this moment come immediately after Dusknoir tells the player that saving the world will make them disappear gives the player a moment to realize what this means- them disappearing will leave their partner all alone again. This scene where the partner pokemon is alone might be an extreme outlier right now, but soon it'll be their whole life. Maybe I'm reading into it too much, but I loved that moment so much and it solidified the game as an all-time favorite for me.