I'm still kicking myself about the fact that I missed 'Metroid Fusion' during the time the GameBoy Advance was the prominent Nintendo handheld. As it turned out, it was the best game in the franchise and the best original game on the system. It even was one of the best handheld games ever. If only I knew sooner, but I had mostly abandoned the handheld and consoles beforehand sadly.
Contrary to earlier games in the series, the game focuses more on the story progression and less on the exploration, though there's still enough exploring to do after the game opens up later on. The story is almost that of a survival horror game, and takes the roots of the series in the movie 'Alien' further than ever before. Famous series protagonist Samus is stranded on an abandoned space station after answering a distress call and finds a species of parasites have taken over all life. One of the parasites takes the shape of Samus herself after she was infected and needed to part with her famous suit.
This antagonist is named "SA-X", and is certainly one of the best antagonists in video-game history. It haunts you throughout the game, and an encounter, even though scripted in the story, is genuinely terrifying. All you want is flee and hide when it appears. The whole game is able to ooze that eerie atmosphere all-around, and had I played it when it came out, it would even have severely helped my perception of the GameBoy Advance system as a whole.