Metroid: Lost Daughter of Remnant.

Chapter 1

Disclaimer, I have not yet played Metroid Prime 2/3 I am currently in the process of playing Prime 1 though. Either way, most of the lore is going to come from RWBY and Dread, so if you haven't watched RWBY, I suggest you do to prevent yourself from being too lost. I'll try my best to prevent that, but no promises.
As for Metroid, There isn't much that needs a deep explanation, so I'm confident in that regard, but spoilers are guaranteed

Samus Aran is a bounty hunter. And her most recent mission had been life-altering to say the least. Even more so than the escort mission on SR388 a few years back. She already got her payment for her mission on planet ZDR from the Federation, and as expected, they did not raise the payment, even after she gave them records of the mission. Not that it matters; that wasn't why she took on the bounty. The threat of the X-Parasites was too dire to negotiate with any real stakes, and the Federation knew that. Hence the absurdly low bounty.
Once she collected the bounty, she immediately left. A lot had happened on that mission. Most of which she didn't dare tell the Federation. What's more is that when Quiet Robe X allowed itself to be absorbed, Samus had gained some of it's- HIS memories. She's not entirely sure how. The parasite that was mimicking Quiet Robe didn't look like a Core X, and even then, she only gained abilities from them, not knowledge. The most logical solution given everything she knows is that either Quiet Robe's Thoha genes gave him some level of control over the X, like they do with the Metroids (Unlikely, given the fact that the X were not artificially created, to her knowledge at least) or, more likely, they wanted to get Samus to leave this universe.
From absorbing that X, Samus learned that she wasn't from this universe, period. She had taken some ancestry tests some years ago, out of sheer curiosity, all of which returned inconclusive, and while tests on her biology did not line up with normal humans, however, she, along with everybody else, just chalked her differences up to the Chozo's genetic modifications. However, now she knew that her biology before Chozo augmentations were vastly different from normal humans.
However, She knows she was born and raised on an Earth Colony, for the first decade or so of her life. She suspects that her birth-parents were the ones who didn't belong. There was a time when she wondered if she had any family. When her parents were still alive, they spoke lovingly of grandparents and aunts and uncles, in the present tense too, but she never saw them. She tried taking ancestry tests and the like, all of which retuned inconclusive. But it turns out, the Thoha sect of Chozo were developing a way for her to go home. And they succeeded. They even made contact with the humans there. Quiet Robe didn't know the specifics because he was elsewhere at the time of contact, but the fact remains that they created a portal to her parents' home universe. While she had long-since made peace with her parents' death, she would be lying if she said she didn't want to learn more about where her birth parents really came from.

So Samus decided to go on another mission. One unknown to all but herself and her AI companion, ADAM. To an uncharted planet, one host to ruins of a once-mighty civilization, now abandoned. A sight she is quite familiar with.
"LADY, WE HAVE ARRIVED AT THE UNIDENTIFIED PLANET"
So this is where they made the portal? "I can see why no one's discovered this place yet."
"INDEED, THE FLIGHT WOULD HAVE BEEN FATAL WITHOUT PRIOR KNOWLEGE OF THE PROPER ROUTE"
The ship lands, Samus downloads Adam to her suit, and she enters the complex. It's not underground, Samus notes. It doesn't take long for her to find a map room. As always, she inserts her arm cannon into the interface, downloading the map of the building. To her surprise, it's very straightforward. A far cry from any Chozo architecture she had seen thus far. She makes her way to the place where the portal lies.
It's a large rectangular room. Samus enters through the right most entrance, nearly flush with the straight wall. The portal resides in the center of the circle, Opposite Samus is the room that is labeled "The Relic" on the map. Supposedly the security for the room is top of the line. She naturally comes to the conclusion that it must have been a gift from the people in the other world. Although why the Thoha placed it under such heavy protection rather than displaying it with pride is beyond her.
She makes her way to the portal. It's circular, with a radius about as large as her. She walks up to the interface next to it and inserts her arm cannon. As she downloads the data related to operation, one document states that a similar device was constructed on the other side to allow two-way transportation. With the knowledge that it won't be a one-way trip, Samus's main concern has been addressed.
The bounty hunter activates the portal, setting it to remain open for an hour, in the event that the portal on the other side is inoperable. The room is bathed in bright blue light, as Samus Aran leaves the universe, not knowing where it will take her.