What happens at the end of Metroid prime 3?

Answer 1

[MASSIVE SPOILER WARNING (obviously)]

Samus and the galactic military people (you know the ones, I forgot the name of the organisation) find a way of creating those worm-holes the leviathan seeds use to get around. They use these to travel to the sourse of the seeds.
The source is a sentient planet they call Phaze which is entirely covered in phazon. The planet is guarded by a large number of space pirates. the Space army people deal with them while Samus lands on the planet. When on the surface Samus is constantly in Hypermode because of the huge amounts of phazon. She travels deep below the surface and fights Dark Samus, then the Aurora Unit stolen from the cosmo-federation ship. the Aurora Unit is entirely corrupted and once defeated all the phazon in the universe becomes inert.
I think that Phaze was attempting to make other planets like itself, which would send their own leviathans to infect other planets, thus phazon would propergate throuought the universe.
Alternatively Dark Samus gained control of the phazon in Metroid Prime 3, so perhaps it was her doing.