Nightshade was seen looking for Shilk not long before the two of them disappeared, having found him near Lavaridge hanging around with the other regulars. During this time she had a short game of seeing whether Jason or another Absol would grow closer to her. When this plan fell through she continued to be her more distant self.
She disappeared alongside her Partner pre-time skip.
One night she appared in the bar, a traveler's cloak around her. She met up with Jason and a Lucario, having seemed to had matured to a more feminine character. Not much is known about what she was doing before arriving in Treasure Town, other than "drifting."
Jason seems to have a very close relationship with her in another world, however she seems to lack the multiverse awareness that he has. Additionally, the fact that he knows so much about her is often both a soft spot and a nerve, leading to different times where she'd physically assault him.