- JOSSED. She's as innocent as Sebastian remembers her and in the end, they get reunited. Lily was taken from the house before it was burned.
- In-game files reveal that Stefano emigrated to Krimson from Italy, meaning he's not a native-born American. There's a larger amount of Spanish-named characters in the first game, Sebastian Castellanos obviously included, but that's a side effect of Shinji Mikami's original plan to set the story in Spain, like he did with Resident Evil 4.
Throughout both games, a peculiar cross-shaped symbol has appeared.
While the two symbols that manifest in the series have their difference, Sebastian recognized the symbol in the second game, so clearly it holds some level of significance. While it bears no resemblance to MOBIUS's symbol, it clearly holds some level of significance to both them and Ruvik, some fans speculating that is a variation of the Beacon Mental Hospital symbol. The first game's STEM system manifests with Ruvik's mind as a base, the prototype built on his memories and his whims. The second game's STEM Union was built to the specific designs that MOBIUS implemented, and Father Theodore was a long time MOBIUS operative.
Perhaps the symbol of MOBIUS's progenitor? Or a secret third party working behind the scenes?
Let's face it, the lack of any frequent references or mentions of Ruvik during the story borders on the deliberate. And while that could be attributed to the developers wanting the second game to be as self-contained as possible, from a story perspective it simply doesn't make sense. Kidman seems to actively avoid mentioning him, with the only casual mention of his name (excluding slides) coming from Sebastian. The only real visual reference to his presence is in Myra's character design, with her "monster" clothing greatly resembling his burnt out white coat and hood. This is, for the most part, left unexplained, but imo, it could be an indication that Myra was somehow under Ruvik's influence during the game.
It's stated that the people who have the most power in STEM are those who suffer from mental disorders that cause them to develop ego-centric, sociopathic personalities. Myra doesn't match that description at all. Ruvik, however, does and if he was somehow influencing Myra then it's not inconceivable to think that he could be "lending" her power within STEM. Hell, if anyone would know how to do that, it'd be him. From what we hear about Myra's plan from Kidman, it was definitely never intended for Myra to become corrupted by STEM. Kidman's "there will be someone in there for you" line to Sebastian implies that she thought Myra would be an ally to Seb from the start. Ruvik's influence would definitely explain how Myra's motivations became so twisted and brutal. It suits his purpose too, in that he probably has more to gain from destroying Mobius than basically anyone else, and while getting Lily out of STEM and destroying Mobius does help him out, making Myra and Theodore exacerbate the situation to such a destructive degree also gains him a shiny new STEM system to build up from scratch.
There's also the question of how exactly Kidman removed her sub-dermal chip. Assuming that the method of chip extraction seen within STEM is accurate, then removal is clearly not a quick and easy process, even on a cadaver. Add to that the fact that the chip must be attached to something important in order to act as an effective kill switch, and you've got a surgical procedure that definitely doesn't lend itself to the DIY treatment. Finding a surgeon willing to perform the extraction is fairly unlikely too, since it's implied that Mobius rules the world to the point of Myra only trusting three confirmed people to help her take them down. So Kidman would need to find a person who had a reason to want to take Mobius down, and who has the relevant skills to perform a delicate extraction surgery without setting off the chip. Ruvik certainly fits the bill there.
We all know that a strange white substance shows up whenever Myra's influence is involved in this game. While it seems sticky like wax, there doesn't seem to be any symbolic connection between Myra and wax unlike the camera paraphernalia with Stefano or the religious iconography with Theodore. So what if it isn't wax. What if it is instead milk, in particular breast milk.
A mother needs to breast feed her children directly after they are born when they are at their most helpless and utterly unable to fend for themselves. Lilly stuck inside the STEM is unaware of her capabilities and totally at the mercy of the those who are trying to control her, and is effectively more or less helpless as a newborn baby.
That said, if a mother continues to breast fed her children as they get older it soon enough becomes a major squick. Thus, the abundance of milk related to Myra shows how her maternal instinct has gotten out of control to the point where she cares more about keeping Lilly all to herself rather than letting her be reunited with Sebastian her loving father or allowed to escape from the STEM.
On the other hand, considering a flashback sequence has Sebastian telling Lily that Myra "can fix anything" then it is also entirely possible that Myra has some Hidden Depths with some crafting talents. The white "mask" she wears seems to resemble a cast or paper mache, and globs of it on the ground look like glue. On top of being less creepy than the above explanation, it also serves to flesh out her character a little further.
The first game states that Ruvik's Amalgams are created from the leftover negative emotions of everyone that died in STEM. One of the first things that Sebastian does is take the recently dead Oscar's revolver. If you subscribe to the theory that Sebastian exerts control over his environment by creating guns, ammo, and supplies, then every time he collects from dead bodies, be it supplies or even the Goo, he's absorbing some part of the long dead Haunted, Lost, and unique monsters into himself, making him stronger.
In the second game, this even manifests as using the communicator as a way to find pockets of leftover power, especially from the bodies of Mobius security. Being specifically trained for diving into STEM, members of Mobius would likely have more willpower than the residents, but most die anyways. Sebastian can sense out their remnants and collect what's left, manifesting as what he perceives to be ammo, guns, upgrades, what have you. Much of the hardware Sebastian carries on him is looted from the dead and could be considered analogous to the stray body parts on the monsters. Both games are the story of Sebastian being put into the STEM, getting his bearings, then gathering power until he can overpower the local psychopaths.