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Pretty sure it is the idea that she was our first ally in the game and guided us among many parts of the game. Then, on second dream even after going against her wishes and flat out ignoring her. She came, in person, for the first time. To help you.
Not that we can fault her, she is after all the reason we, the tenno, went on a genocide against the orikin.
Now. Some lore. As we all know. The "Orikin", the creators also know as the ones to have made the tenno. Are the human race. It ties in a similar way to the plot of Halo.
Anyway, The Orikin. The pinacle of humanity, we created the Grineer, Infected, and Sentients. The corpus are just the remains of our race. Which have become more akin to dog breeds in which the credits and commerce are what makes the breed higher.
Grineer, clones made to get easy organ replacement and slaves. The Sentients, terraforming machines. The Infected were created to fight The Sentients after they rebelled.
After the sentients rebelled against the Orikin. They created the infested. The infested didn't work as planned, but they were close. So, they created the Tenno. Fusing both the power of the infestation in armors, and young humans. They made, the first Tenno. "Machines" to fight the sentient Hunhow or something. Too bad, the Orikin saw the Tenno as too powerful, and wanted to end them. Too bad for them, that "Marculis", also know as Lotus. The only mix of a Oriking with Sentient powers, the "daughter" of Hunhow. Took pity on us, and wanted to help us. It was because of her, that we Tenno rebelled against the Orikin. We brough them to extintion. Then... we went asleep. But the Lotus, as always. Just wanted us to "live". Knowing our past was not really something that we needed. So she was against the idea of us confronting the past. Because, for all intenses and purposes. Lotus send us on a path to end the Orikin. We almost succes, some remain. But the golden days have been left behind. They are no better than Grineer clones. Corpus is what we call them now.
That is what I got from the forum and the Wiki. It's higly hypotetised that Ballas did something to Lotus to change her mind. Some say he woke up the "sentient" inside of her. Which would explain what happen to Ballas and why she wants to, well. Terraform the solar system and end every other race? For all we know it is Hunhow's dead man switch that ballas activated inside of lotus.
Sorry I didn't know how to quote a smaller portion of your reply. You wrote such a good and concise summary of the lore.
However, I want to correct you a bit (of course I can be a bit wrong I'm also contributing to a fan summary). When you say after the Orokin made the infested, that they made the Tenno, that is not true. The word I am sure you meant to write there was not Tenno but warframes. "So, they created WARFRAMES". Warframes are made from the same amalgamated-biological engineering technology that enabled the Orokin to design the infestation. They also couldn't control or effectively use the warframes to fight the sentients or infestation, despite their power--either that or despite their power they were still losing. Not to mention the Orokin (Ballas particularly) turned some people into Warframes as a form of extra-judicial punishment, resulting in them being even more difficult to control.
I don't the order of these next things but they: a) discovered that void energy was poisonous to the sentients, and b) they experimented on the children of the Zariman Ten Zero, a mobile space colony that was bathed in the void--thus creating the Tenno. Basically a race of people and their descendants who can use Transference to move their consciousness through the void or control void energy and Warframes. Natah was borne by the sentients as a mimic, and sent to the Orokin (origin system) to destroy the Tenno as the Tenno were the Sentients biggest weakness. The Tenno are warriors and manipulators of the Void's energy. They are direct descendants of people who were exposed to the void and survived, and in some cases they are the same people who survived the Zariman 10-0. The Tenno were the people responsible for helping the Orokin win their first war against the sentients.
It is potentially implied that Ballas discovered the identity of Natah before anyone else, and upon Margulis' execution he uploaded, or programmed or telepathically implanted, Margulis' memories, or fragments of her consciousness, into Natah. Natah/The Lotus explains, afair, as you're running to the Ropalolyst, that those memories were like warm light in her mind, blinding her to her past. She also seems to explain that despite the manipulation, her relationship with the Tenno is real--that her time spent with us affects her despite her reawakening as Natah. Possibly because of tangible links to Margulis' original mind inside her own or because of her own feelings. I took what she was saying as her saying her feelings for the Tenno persist despite her true memories having come back partly because, as she explains, she is sterile and truely felt like a mother to us whether or not she was of her true mind.  And she has mixed feelings about this motherly relationship, as she recognizes it may only be because her journey to the Origin System left her sterile so unable to reproduce.
I just wanted to correct the Tenno/Warframe thing in the order of your lore dump. Then I got carried away filling stuff in haha. Cheers.Â