I want to add one more thing to what I said above when I gave my explanation as further evidence. This is all from in the game itself!
As we all know, Natalia became confused because Alex's memories were merging with hers and Alex's consciousness was trying to take over. They are of course their own individuals and the real Natalia is trapped inside and will clearly try to fight to be herself again post Rev2 (this is obvious) and be a complete pain in Alex's ass. I'm sure Alex will be trapping Natalia with horrors to keep her drowned and possibly try to destroy her consciousness so there is no resistance. In the end I think Natalia will either win and defeat Alex or force her to find another body... such as Sherry's who would be perfect since the G-Virus bonded with her and she will live for up to 400 years. I wouldn't be surprised if Alex sets her sights on Sherry at some point >.>
Anyways back on track to what I wanted to point out. That Alex shows a sign of confusion and perhaps multiple personality disorder near the end. The final document of the game and what Alex says explains A LOT! Alex was thankful that reawakened as herself so she could fix the mistake, that mistake was Natalia.
Spoken bit regarding the True or False:
"I alone am true. You are false Natalia."
"You reject what was given to you... You reject your memories.... False!"
"Begone False one."
Now the document is confusing because it can be taken as evidence for both sides of the argument. HOWEVER once you realise that "She" refers to Natalia and NOT the Alex within Natalia. Everything begins to come clear and Alex wants to awaken. I'll explain it paragraph by paragraph.
"I survived... My escape wasn't death. I have no one to blame but myself"
Alex's escape wasn't just death. It was to Awaken within Natalia and destroying Natalia's consciousness and being only her! The one and only Alex.
"When I pulled the trigger... in that instant the thought of vanishing from this world.. Me! Me of all people... I came to feel fear."
This is why she mutated and she felt fear because what if this was the end and the transfer was a failure?
"How ironic. The viruses inside of me... rotting away my body to the point of death, saved me from death."
People seem to think this only refers to the T-Phobos virus. This is untrue and it says "viruses". While she survived the Prototype Virus from Project W. it made her sick and this sickness was killing her. She did not have much time left and she needed to find another means of immortality once she realised that the body will age is an inescapable fact. Resident Evil 5 stated in the Ndipaya tribe file that even those who bond with the Progenitor virus will only have prolonged life and their body will shut down centuries later. Alex knew this and she then poured all of her resources to find an alternative. She cracked it and succeeded where everyone else failed.
"I have become ugly. Hideous. I can't stand the sight of myself. This isn't me. This ugly creature..."
This one is very self-explanatory. She is very angry about her monster form and she states that it isn't really her.
"But soon another me will awaken. The vessel I transferred myself into."
This is obviously referring to the transfer and how she, Alex, is now in Natalia's body but had not awaken yet.
"I won't allow it. I forbid it. She is the ugly one. Yet she'll look at me and laugh at how hideous I am."
This line is confusing as it contradicts pretty much everything else. However it could be a result of confusion and arguing with herself in the sense of multipersonality. "She is the ugly one." is clearly referring to Natalia, where the "she'll look at me and laugh at how hideous I am." likely refers to the Alex within Natalia BUT could be referring to Natalia as Alex's memories are bleeding into Natalia's.
"Why have I become so hideous?"
Alex is ****ed the **** off!
"I am me. But I am not. I awakened as myself. But then she will also awaken as me. Both are true."
Alex says that she is me because she awakened as herself. Then she states that she is not her because there are now two of her. She wants the Alex within Natalia to be her and not the monstrous form that she is in. Both are true and she wants to fix this "mistake" and be whole again.
No! There can only be one true me. And that is me! She can never be me. She is false. She is a farce. That is why she cannot be allowed to persist. She must be eliminated."
Alex wants to be whole again and is concerned that Natalia's consciousness will be in control with Alex's memories bleeding into Natalia. Alex calls Natalia a joke and that she must be eliminated so only Alex can exist in Natalia's body and only Alex alone is true!
"I am me. Only I am true. I'll use that abomination. Albert's final legacy. I'll smother this insufferable island with Uroboros. She will be eviscerated. She will come to know fear. You will feel the icy embraces of death... Natalia..."
Alex is once again stating that only Alex herself is true and that Natalia cannot interfere with her and she won't let Natalia become her due to memories bleeding (the memory bleeding effect has occurred multiple times throughout the game and Natalia has become confused by it more than a few times). Ironically even Alex thinks Uroboros is a **** virus "I'll use that
abomination." LMAO. I'll admit Uroboros had a dozen flaws with it but this is not important, just part of what she is saying. She will use Uroboros as she has modified it to infect the island to further scare Natalia and make her feel fear! (it was stated earlier in the game that Natalia has conquered fear and is incapable of feeling fear). She will ensure that Natalia will die. In the bad ending of the game the monster Alex is "eviscerated."
"And then, when you die false one, I will take your body. I will become the true me. Natalia... you must die.."
This right here is the final word and the most important quote in the whole game to prove that the Alex within Natalia is 100% is the real Alex and one and the same. Alex wants to make sure that Natalia's consciousness is dead and gone from this world. Alex and Alex alone will be the true Alex in a new young, beautiful, and extremely capable body.
It is true that in the good ending Natalia is still alive and having a tug-of-war with Alex.
I believe that the bad ending was created to show that Alex without a shed of doubt won and succeeded no matter what ending you got. To clear confusion so to speak.
In the bad ending we see that Alex kills Natalia. We see Natalia's arms, head, and legs go limp. We see the result of what happens when someone dies and their consciousness is no longer functional or present in their body. Alex crushes Natalia with so much pain that her body let up and she died. Once Natalia was dead, the Alex within her kick-started the body and took complete control. Alex then eviscerated her old body and became whole again, the one true Alex. Exactly as the document above stated would happen. It is odd how the powers within Alex transferred as well, while this isn't exactly logical, it happened. Alex's new body isn't sick and can now have the powers that were always hers but were previously inaccessible due to her illness. In the end there is just to much evidence in the game that shows that
Alex is Alex!