When Vanya lands in the '60s, she has no memory of her siblings or any of their adventures. She winds up as the caretaker for a boy named Harlan, living with her parents, Carl and Sissy. Vanya and Sissy grow close, the two falling into an emotional affair behind Carl's back that leads to a heap of trouble when he discovers their secret. All the while, Vanya's siblings find their way back to her, explaining the insanity of their lives in a way that she glibly accepts.
Without the firsthand knowledge of all the pain from their childhood and their struggles in the first season, Vanya's control over her powers is more finely tuned. But when she's arrested by the cops while trying to escape with Sissy and Harlan, she's taken to the FBI who suspect she's actually a Russian spy. The interrogation turns to torture and drugging, which causes Vanya to slip into a trance. While under, her nightmares cause an outburst of her powers similar to the one in season one that destroyed the moon. She kills everyone in the building, and though Diego, Allison, and Klaus all attempt to pull her out of it, it's Ben who manages to bring her back.
Now, all the Hargreeves are wanted criminals in the eyes of the law, which is just in time for Vanya to realise that Harlan is in trouble back at Sissy's farm. Vanya managed to push some of her power into him while performing CPR on him earlier, and not his body is on overload. When the siblings arrive at the farm to help, they're ambushed by the Handler, Lila, and Commission agents. Once the dust dies down with the Handler and a time briefcase secured, Vanya takes back her power from Harlan and the siblings' journey back to 2019 without him and Sissy. We see later that Harlan still has powers, as he's seen telekinetically making his toys float.