Wondering how you ended up from being next to Bruce to being locked in a room protected by militiamen, tied to a chair? It's simple. Both the Arkham Knight and Crane needed the bat's attention, so they used his only weak point. You, one of his most trusted allies along with Robin and Alfred.
Bruce fell into Scarecrow's trap very well. After both Crane and the Knight captured you, they could say they had the bat in their hands. And it was true, partially.
Slowly you opened your eyes and regained consciousness, and you realized that you had a blindfold over your eyes and were tied to a chair. Great.
Suddenly you heard a door open and heavy footsteps getting louder and louder as the mysterious figure approached. Then, in a flash, someone ripped the bandage off you, almost aggressively.
You immediately recognized the Arkham Knight. He let out a low chuckle and looked at his soldiers, his gaze hidden by his helmet.
"Keep her here and don't let your guard down." He spat these words and turned to leave, but then stopped.
"The first one who touches her is dead."
Obviously he didn't want you dead, he needed you. He hated you, he was just exploiting you. That attention to you was just for convenience.
Or, at least, that's what he likes to believe.