Contemporary Pokemon storylines from that time period were getting a bit stale and predictable. Bad guy awakens minor diety, nearly destroys world, child player character steps in and saves the day. Woohoo. There's only so many ways you can tell that story before it gets kind of old. Explorers, not being a traditional Pokemon game and therefore not being bound to the same story beats, throws that out the window. There's still the huge, climactic conclusion to the story as you fight a minor god to save the world from a fate that's arguably worse than simple destruction, but Explorers earns that so much more than other games in the series do.
So the first thing Explorers does right is the pacing. The pacing of traditional Pokemon games can also be sort of strange sometimes, and this is a problem they seem to struggle to fix (Sw/Sh is the perfect example of this, but even games more contemporary to Explorers had this problem to a lesser degree). The main villains usually show up a few times doing something of little to no consequence, then when the climactic point of the main story comes you have to deal with them for a solid chunk of time, then they sink back into the background. They've got this weird bell curve of involvement that I don't really like.
Explorers doesn't do that. You get a couple cutscenes of who you think is the main villain doing something your trusted partner tells you is so bad even the worst criminals don't do it, but never do you battle or even encounter Grovyle face-to-face until the build-up to the main climax of the story is starting to ramp up. The game doesn't throw him at you a few times in the early game like it usually does with evil team grunts and admins. Instead, that role goes to Team Skull (the original Team Skull), who act as sort of your rivals for most of the game but ultimately aren't very consequential towards its main storyline. The entire first half of the main storyline doesn't actually have that much to do with the main conflict, and that's okay. It introduces you to the world, it introduces you to some of the characters, it lets you get familiar with the game's mechanics, and it gives you some fun little missions to do even if they aren't ultimately all that important.
Then it throws the action at you, fast and hard. That bell curve becomes a proper slope.
Then, once you you've finally outsmarted the main villain and foiled his evil plans... the game throws the biggest curveball in the entire franchise at you and reveals that he was the good guy the entire time, and the seemingly wise and benevolent Dusknoir is actually an agent of darkness working to preserve a paralyzed future where time has stopped, plunging the world into a state of permanent darkness and decay. That's the other thing Explorers does so much better than other games, not just other Pokemon games but honestly other games in general; its plot twists. There's several of them, and they're huge and well-earned.
This is actually one of the things I hated about Gates is it essentially copies a lot of the same beats as Explorers, including some of the plot twists, but it seems way more artificial in Gates. It's like they thought, "Well, they liked it when we did it in Explorers, so we'll just do it again!", but that's lazy in my opinion, and doesn't lead to an organic-feeling plotline. Super Mystery Dungeon does much better in this regard. There's still a couple plot twists, you still get backstabbed by a character you thought was an ally, but there's no real direct equivalent to Grovyle in that game, and they do a much better job at disguising who it is who ultimately betrays you, and adding interesting new beats to the story along with subverting one of the usual plot twists. Overall it feels a lot more creative, while still hitting some of the beats that are practically tradition within the Mystery Dungeon series at this point.
Another thing that Explorers does well is the characters. Well, mostly. At a time when Pokemon characters were too often bland and frankly soulless, most of the important characters in Mystery Dungeon have personality. Grovyle turns out to not be the generic bad guy you first think he is, but he's also not really a generic good guy either. He's rash and he's willing to follow his mission through at all costs, threatening Azelf's life when he seals away his Time Gear. He doesn't try to reason with the Lake spirits, he doesn't explain who he is or why he needs the Time Gears. Maybe they wouldn't have believed him, but maybe they
would. It would have at least been worth a try to avoid violence, but Grovyle doesn't. He immediately attacks them. Sky fills out Grovyle even further, explaining his motivations for wanting to prevent a future of darkness, even if it ultimately means giving up his own life. Despite being from a harsh future of unending darkness and decay, something that explains his rashness and tendency towards violent solutions over peaceful ones, he's ultimately a good, selfless Pokemon who's willing to sacrifice himself for the greater good of the entire world; one of the only ones who seems willing to make that sacrifice, in fact.
Then we have Dusknoir, who initially seems charitable, wise, and benevolent, saving you from a dangerous situation Team Skull lands you in at no real benefit to himself. As it turns out, he's deceiving you and is actually motivated purely by self-preservation, but here's the thing; I actually really like Dusknoir as a villain. He's actually very relatable and sympathetic if you think about it.
Let's do a little thought experiment real quick. Let's say you have the opportunity to travel back to the dawn of humankind and permanently erase the concept of war from human history, but as a result the timeline you exist in is destroyed. You, all of your friends, your family, everyone you've ever known and cared about, gone for the sake of a world you'll never live in. It would make that world objectively better, but at the cost of yourself and everyone you love. How many of you would actually do it? How many of you would be able to fault someone who
doesn't do it, even tries to prevent other people from doing it? Is that selfish? Sure. But is it evil or unreasonable? I don't necessarily think so.
This is the position Dusknoir finds himself in. He's presumably never known anything but the world of darkness. Everyone and everything he's ever known exists in it, and now Grovyle and the main character come along and threaten to destroy that to restore a timeline that none of them can exist in. Who can really blame Dusknoir for standing against them? Self-sacrifice for a greater cause might be a virtue, but is not having the strength to sacrifice not only yourself but everyone and everything you've ever known really a fault?
The minor characters tend to be a little less fleshed out but I'm fine with that. It's hard to make a few dozen characters all crazy complex and interesting without the story seeming bloated and unfocused. The important characters are deep, the not so important characters not so much. That's an efficient use of plot time in my opinion. Plus, Sky does remedy this a little bit with optional special episodes for some of the minor characters, including a satisfying conclusion for Grovyle and Dusknoir's story.
Then we get to the soundtracks. PMD2 has, in my opinion,
the best soundtrack of any game in that time period. Yeah, I know, controversial opinion, but I stand by it. It's put to excellent use, too. Emotional moments in the storyline (which there are plenty of; some of them even hit quite hard if you're really immersed in the story) are always set to a very somber, emotional track, and it really amplifies their impact. Action-packed moments are set to very energetic music, subconsciously preparing you for a tough fight. Tough, gruelling dungeons have tracks that sound almost like training music, while more laid-back ones usually have more mellow, peaceful soundtracks that bring forth vibes of exploration and discovery. The final boss in the main story has what I still consider to be the single best soundtrack in the entire franchise, and it really helps sell the desperation of the fact that you're a pair of measly little first-stage Pokemon facing up to a rampaging diety. Even hopeless moments in the game's storyline where it seems all might be lost are usually set to
this masterpiece, which fits the mood perfectly. I can think of no other game that both has amazing soundtracks like PMD2 and uses them as well as PMD2 does.
Finally we get to some of the fundamental concepts Explorers's story includes and talks about. Explorers's story is about many things, really.
It's about friendship, which most Pokemon games are about, but it does it so,
so much better than main series Pokemon games. By having a partner who's constantly there for every moment of the storyline, who sometimes needs your support the way every friend does, but ultimately pulls through and has your back at every crucial moment, and who experiences significant character growth influenced heavily by you, it's very easy to get attached to them in a way that most characters from most games struggle to endear themselves to you. For many people, especially those who played the game at a young age, by the end you really
don't want to say goodbye. You really do feel like you're parting ways with a trusted friend. You really understand the sacrifice your character is making.
It's also about life and death, and the true value of one's life. This is especially impressive when you consider that death was a concept almost entirely absent from the main series during this period in the Pokemon franchise. Never is the word 'death' even used in the Explorers games; instead characters threaten to 'destroy' you, 'eliminate' you, or 'force you to disappear', but the end result is the same, and so it finds an excuse to talk about the same concepts. It talks about the pain of leaving those you care about behind. It talks about their grief in your absence, the impact a sudden loss of a close friend can have. It talks about what one's life is really worth, not to others but to
themselves, and what they might measure it by, what they would sacrifice it for. What it
means to live. It talks about sacrifice, heroism, selfishness, self-preservation, and redemption. You even help your partner through a brief period of suicidal depression at one point.