Initially I wanted to put the discussion flair on this post, but due to this containing major spoilers, I decided with Spoiler instead.

Alright, so I've played through all the quests, and I do understand how warframes came to be and why transference exists and who we Tenno are.

Now, my question refers to the backstories of individual warframes, and what they are in the present.

You see, based on the lore, the backstory and mind of each warframe can be put in a specific phase.

1: Turned into a warframe, but still loyal to the Orokin. (Ash probably fits this one)
2: No longer loyal to the Orokin, but not yet tortured.
3: Tortured, uncontrollable.
4: Controlled by Tenno, loyal to the Orokin.
5: Controlled by Tenno, loyal to the Lotus.

My assumption would be that every warframe fits one of these phases. It's curious that Ballas considered all the warframes to be failures since they turned against the Orokin, so maybe some took longer to turn than others, but eventually they all turned?

My main is Gara, so I looked into her lore... and I noticed something curious.

You see, her legend says she was a close companion to Unum (in Cetus' tower) and that when the Lotus told the warframes to retreat, she stayed to protect Unum.
This'd put Gara's backstory solidly in phase 5.
But, if Gara is controlled by the Tenno, then she wouldn't sacrifice herself. It'd be the Tenno sacrificing the warframe.

Then, since we as Tenno did not have access to Gara before we found the blueprints, it'd mean that when a warframe gets destroyed, it's no longer available to us.

Warframes are living beings infected with the Helminth infestation strain. It's logical that if the warframe gets destroyed, so does our access to said frame. As the living being that was turned into the frame is also destroyed.

How the hell are we creating frames in our foundry then? Are these replica's of the original? Are we reviving people and simultaneously turning them into warframes? Are we bringing back tortured souls so they can continue living in agony with our transference giving them some respite from said agony?

Are we the baddies? :P

In all seriousness... I do believe this is game design clashing with lore and am wondering if any lore is established to explain said game design?

Oh another example is Titania. She was a phase 2 warframe. Protecting Silvana, and killed by Dax soldiers. We get her blueprints and craft her after the questline. So we essentially revive a warframe that has yet to be tortured, but we still have transference to them. From my understanding transference is possible because we found a way to look inside the ugly broken thing and take away their pain.

Anyways, let me know your thoughts as I continue pondering this.