What, Nintendo games have stories? I thought they were just about jumping on platforms and collecting coins and stuff, maybe with some tacked on goal of saving some princess, which somehow is achieved by the aforementioned jumping around and collecting arbitrary things. Basically Tetris-level storytelling?
Just kidding, don't lynch me. I guess at least the occasional RPGs have stories and an actual plot, right? What about Zelda games? Metroids seems to be about shooting stuff, but are there cutscenes or screens or even dialogue that tell a story at the same time so that it's not just shooting for the sake of shooting? I'm not being snarky, this is my honest and a little ignorant perception of Ninty games.

Eternal Darkness

Xenoblade Chronicles + Fire Emblem

Best Nintendo Story? not really a Oxymoron but close... most of their games are pretty light on story.

I guess it would be one of their RPG games, like TTYD or Super Mario RPG.

Skyward Sword IMO

I'd have to say Earthbound, Mother 3, Skyward Sword, Xenoblade Chronicles and Majora's Mask in terms of 'traditional' story (e.g. cut-scene driven narrative). I haven't played many of the older Fire Emblem games so I'm interested that a few people put those as being strong narratives. I have to say I preferred Shadows of Valentia's pared-back approach in terms of narrative and aesthetic over Fates's smorgasbord approach, and felt while the narrative was simpler, the twin-paths approach was really engaging. It's one of the stronger (recent) story-driven Nintendo games I've played.

In terms of world-driven story (atmosphere, aesthetics, architecture, environment, optional back-story) I'd say Breath of the Wild, Super Metroid, and the first two Prime games. None of them do much cut-scene wise, and none of them thread a persistent overt narrative into the game in a particularly strong or consistent way, but in terms of what you can learn simply through playing I think they're first-class.

XC

OOT.

A Zelda game, take your pick.

I love a good, classic 'good-versus-evil' story already so things like A Link to the Past, Ocarina of Time and Breath of the Wild are winners, but then the games where they go into an opposite, deeper direction like Link's Awakening and Majora's Mask truly shine. Those are top-tier for a video-game in general if you asked me.

Of course?Inteligent Systems is 100% owned by Nintendo.They are the same as the EADs.