Allright, this is probably already thought of before, but since i couldn't find something about this anywhere i decided to post it. Here we go...

My theory: Metroid Prime IS Mother Brain. Both look the same (at least the mother brain in the original Metroid, but i haven't played SM, and this is set before Metroid II and SM anyway), blue with red tints and vessels. They both wear the Phazon Beam -- or the one in SM suddenly possesses a "Hyper-beam" that is a lot like it. Furthermore, a "great asteroid" full of phazon blasts into Tallon IV. Zebes's Tourian was destroyed -- could that not have set off the asteroid? It was big enough for Tourian by far but too small for a substantial chunk of a planet. My theory is that Mother Brain is also a metroid-like -- the Chozo engineered both, so what once works kan work again. That it's cybernetic this time doesn't make a lot of difference -- except it needs a "shell" to survive long. Glass case in Metroid anyone? Furthermore, this would explain (if there are Save and Missile stations in ZM, i haven't played that one), at least partly the technology present. And who says that we have seen all of zebes at the end of even ZM? There could be an entire unknown facilitiy which we do not know anthing about. Also, the Mother Brain explodes but survives, and later seems to be part of a bipedal creature. Yet most of its brain must have been intact, otherwise it would make a few weird jumps en die. Metroid Prime could make herself invisible -- who says she didn't posess that trick in the original Metroid? Furthermore i theorize that Mother Brain must have gone kind of mad (incident?) at Tourian, which would explain the weaponery she obtained. I don't know the NTSC logs exactly by memory, but did they actually say WHERE MP was contained? Also, we have this marvellous MP that is rumoured to produce its own sustenance -- phazon! (or hyper, if you prefer :P). The phazon could even be the "life energy" the metroids suck out of living beings, altough i am not exactly certain. In any case, Metroids seem to react well to creatures infused with phazon -- if Mother Brain had endlessly infused herself with phazon, and the metroids contain that energy somehow also, it could explain the soical behivour of these creatures. Furthermore, if the ship originally carring the Metroids pre-game, had X onboard it? It would infect a few space pirates, and nothing is revealed _at all_ about the final happenings of the original Federation Metroid research vessel. Some could have easily traveled back to SR388 -- with their new forms, they could easily have hidden from the Metroids. Until Samus in Metroid II begins interfering with the plans of the Metroids -- and lets the X loose, which explains the X-infected space pirates on the B.S.L. station! And it is perfectly possible to find te space pirates capturing MP again at the end of MP3 -- after she is finally finished off by Samus.

That's all the evidence i can come up with right now, and i certainly have dropped some points, so i'd like your suggestions on this one :P