Cez, you didn't even answer the question. Look, I'll give the answer:
After Samus defeated Metroid Prime's second form in Metroid Prime 1, the whole thing transormed into a large globe of shining Phazon energy with tentacles. It whips out at you with one of the tentacles, sensing the Phazon in your suit. That is where your suit is degraded back to the Gravity Suit, as the large creature absorbs the corruption within your Phazon Suit... absorbing your DNA in the process. After escaping the crater collapse, if you have collected 100% items in the game, then you will see a black hand with an eye on the back of it reach out of the crater. That's when you fly away.
That's when Dark Samus was formed. Metroid Prime had your DNA, and mixed that with the Phazon energy it could produce, and came out with Dark Samus. If you look at the backside of Dark Samus's left hand in Metroid Prime 2 in the scan results screen, you will see an eye on the back of it- just like when you saw in Metroid Prime 1 after esccape from the crater...
That is also why Metroid Prime 2 is called what it is, because there would be no purpose in calling it 'Metroid Prime 2: Echoes' if Metroid Prime had nothing to do with it, and it sure did, creating Dark Samus.
Owner of the formerly ranked number one Halo PC modded server in the world, FRIGID MASS CTF WAR. Joiner-friendly mods and five-minute hotfixes = loyal clientele.
Been here since February 2004. It's May 2022 as of writing this. Wish Rich would revive this place. Guess I'm only here for the nostalgia now.