Shadow had helped you escape from Nine during a fight and you went to New Yoke City for help to defeat Nine. However he didn't stop trying to get what he wanted, and he wanted your energy. So he sent his bots after you, while also making sure you stayed in one place by turning New Yoke City left and right constantly so you were running around trying to save everyone. And eventually he appeared again as a hologram.

"I'm tired of waiting for you to accept your future. Bring them to me alive."

Nine commanded his bots then he disappeared and soon enough you were being dragged by one of his bots to the Grim where his Citadel was.