Sometime after the disaster on the ARK, Nyx the Shoebill was created by Gerald Robotnik's son (Let's call him Steve Robotnik, as a reference to Sonic Boom.) after coming into possession of his journal. Assuming Shadow was destroyed by G.U.N., Steve created Nyx (Named after the Greek goddess of night, offspring of Chaos.) in secret, with the sole purpose of avenging the death of his daughter, Maria.
Nyx was created with Black Arms DNA, like Shadow, though she was never made aware of this, and trained in Steve's compound on the moon (Just go with it, ok?), learning how to use a weapon, how to harness chaos energy, and how earth deserves to be destroyed.
One day Steve puts Nyx in stasis before he leaves, common practice, and never returned for unknown reasons. Nyx was left in stasis, until Eggman's demonstration of the Eclipse Cannon on the moon, where all remains of the third iteration of Project Shadow were destroyed.
But this is an AU, assume Eggman never you-know-what-ed on the moon. Nyx was left in stasis until the arrival of the Black Comet, when she was reawakened by the presence of Black Doom.
Now awake, she re-explores the facility, realizing how much time has passed. She briefly mourns the loss of her mentor before a, bright flash from outside catches her attention, the Eclipse Cannon being used to defeat Devil Doom.
Assuming it's just pointless earth war, she is filled with rage, and begins planning her escape to earth.