To answer this question you'll have to know the revelations of Metroid prime 3
When the Leviathan (the creature/meteor that crashed into the planet) created a wormhole to appear near the planet; due to the unstable energy of Aether, the Leviathan ripped open the dark dimension and crashed upon it. This rip was still open and so the portals could let them go through it, in reality there always were two planets its just that the rip let them see each other.
Not only that, but the energy contained in this particular Leviathan was much more concentrated than any of the others seen. The force of the released energy was more than enough to split the already unstable planet.