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Guessed by @Ultrashroomz
The trilogy was long finished, the story arc brought to a satisfying close with a game widely heralded as a masterpiece... and then they made another. It's a well-known recipe for disaster. Metroid Fusion did everything we expect the crappy sequel to do: It changed the tone of the series, making it more story-heavy with tons of dialogue, continuing a story that needed no continuation, changed the level design the series was known for in favor of a more linear approach, and tried to recontextualize everything we saw in previous games with a new level of "everything was connected" retcon, you know, the stuff that never works.
And then, it worked. Everything worked. The retcons to the lore of previous games made sense and was exactly as mindblowing as they wanted it to be. The dialogue-heavy style worked to create a story far more engaging than we knew this series could do, and a genuinely intriguing story at that, allowing us to get to know more of Samus underneath the suit, without ruining who we see her be from the outside. And the linear level design, if done mostly in favor of that story, ultimately worked to get a game that played very differently from other Metroid titles, one that could deliver focused moments of tension through scripted scenarios and increasingly harder boss fights.
Fusion was a radical, bold new direction for the franchise, and it was the game that truly established what is possibly the greatest quality about the Metroid series: it changes. These games all have an identity of their own, a distinct tone and style, and none stand out more than Fusion. You could've forgiven the developers for trying to outdo Super Metroid, instead they went in a completely unexpected direction and made the entire Metroid series far more interesting in the process.
