She still gets shot and sends Shadow to earth, but this time she just doesn't stay dead due to the Black Arm cells (from Shadow's blood) she's been infused with by her grandfather. Gerald did this in a last attempt to cure her as he feared GUN would soon come for him and his research- he was right of course...
The cells mass multiplying to save the host have changed her body, slowed her aging significantly. Spending a large part of the last 50 years hiding away from GUN after escaping their facility thanks to the commander (once he reached a high enough rank to even discover she was there), she doesn't really look as kindly upon humanity any more.
Even though the commander claims Shadow was never found ( and likely dead) she is is searching for him endlessly, becoming very science savvy in the process and gaining full control over her grandfather's creation, the artificial chaos.
She can sense Shadow is alive, the black arm part of her sharing a connection with him. However, this connection also extends to Black doom and when he returns to earth he becomes aware of her. Unlike Shadow this human "child" is far more susceptible to his mind control and influence.
Shadow in turn might not fully remember everything, but he feels a strong bond with Maria, in more ways than just his lost memories could explain which confuses him. Since she's on the side of the Black Arms, going against them will become a lot harder for him. Hopefully Sonic and/or Rogue manage to get through to him, or earth will have an issue.
Outside of Black Doom messing with her head her goal is to live with shadow on the ARK, away from the humans that could hurt either of them. Black doom offering a way for them to be able to live on earth itself without the threat of humanity coming after them (after all of humanity have become part of them- he meant as food, Maria thought he meant like she was, infused with their essence) did plant some ideas in her head however, even after their defeat, maybe she'd take a page out of Eggman's book and want Marialand, using her grandfather's memory altering tech to create a way to keep people in line.
germansingergirl
s-u-f-j-a-n-s-t-e-v-e-n-s
ellievsbear
gummygunk
origamiaround
