Metroid II: You (Samus) wiped out all the Metroids, including the very last one in the game. Well, that was your mission - so, whatever. Onto the next game, as it's revealed... UH OH - Mother Brain and her forces of evil monsters are back to take the universe! Onto Super Metroid (If we can even call it that.).
Super Metroid: You've been dispatched to eliminate Mother Brain on Zebes (skip Ceres Station, because there's no last Metroid to keep Ridley from getting his talons on.); you reach Mother Brain - she reveals her second (true) form...
YOU DIE, as nothing you have can beat her true form and there's no grown-up Metroid to save you, because you (Samus) wiped them all out! Including the one that could have saved you and the universe from Mother Brain (and her army of evil monsters)'s tyrannical rule over said universe. Have a nice afterlife, my dear Samus.
AND WITH THAT, GAME OVER.
However, by some miracle pulled outta your ass, you did beat Mother Brain in her second form without the last Metroid' s help... Well, you're gonna die in the next game! And with that, onto Metroid Fusion.
Metroid Fusion: You (Samus) are killed by the X Parasites on SR388, because, again, there's no Metroids to save you in any way, shape or form, not even as a cure for the X Parasite infecting your ass. Because, again, in Metroid II, you wiped out ALL the Metroids, including the one destined to save you in Super Metroid, as well as that same one destined to become experimental medicine in case you ever got infected with something like that of the X Parasites!
So, you beat Mother Brain (somehow...), but now it's the X Parasites that rule over the universe. The same parasites Metroids are beloved for being predators to their prey and helping to keep the universe safe from.
AND that's why we don't wipe out the Metroids, everyone. Again, have a nice afterlife, Samus.
OK, NOW IT'S GAME OVER FOR REAL.