Similar to how both of yesterday's game were kind of the black sheep of the Metroid franchise, today's sort of follows a theme in that they're both sequels in the Prime series. Both of these game are great, and it was actually kind of hard for me to rank one of these higher than the other but I did it.
Once again, SPOILERS!!!!
Furthermore, Samus herself has been infected with Phazon which is slowly corrupting her body. As she travels from planet to planet destroying the Leviathans, the corruption continues to progress. Along the way she is forced to defeat her fellow bounty hunters which had already succumbed to their infection. After taking down Omega Ridley in the Pirate Homeworld Leviathan, the Galactic Federation launches an assault on the planet and discovers the location of Phaaze.
Upon landing on Phaaze, Samus becomes so corrupted by the Phazon that her own ship doesn't recognize her. This forces her to act fast, and she meets Dark Samus for one final showdown. After the latter's defeat, she escapes Phaaze, the Phazon threat ended once and for all.
Prime 2 I've already given the story for, so here's a quick recap: The planet Aether was split into two dimension (light and dark) by the aforementioned Leviathan, and the inhabitants of Dark Aether, the Ing, drove the Luminoth to near extinction and stole the Light of Aether, an energy source that keeps the planet stabilized. Samus is asked by U-Mos, leader of the Luminoth, to assist them in bringing down the Ing Horde and returning the Light.
Along the way she encounters both Space Pirate forces and her doppleganger, Dark Samus. After returning all the Lights, defeating the Emperor Ing, and besting Dark Samus one last time, Samus leaves the now peaceful planet to embark on her next mission.
Like I said, both of these games are great. I've got to give Prime 3 props for having such great bosses (Meta/Omega Ridley, Rundas, and Ghor), as well as some beautiful worlds to traverse. The music is definitely great too.
However, I feel that Prime 2 had a better backstory with the Luminoth-Ing war, and discovering that lore was what really pushed me in my mission and gave me the determination to end every Ing I came across. Plus, I'm a huge sucker for inter-dimension games (I ABSOLUTELY love A Link to the Past, and now I have it in Metroid form!).