The Arkham Knight kidnapped you, literally dragged you away and tied you to a chair in his headquarters. Why, you may ask?

Let's take a few steps back. After his death, Bruce replaced Jason with a new Robin. A Robin completely different from him. He then returned to life and took on the identity of the Arkham Knight. He started spying on Bruce in Arkham City and after that he finally declared war.

He teamed up with the Scarecrow to find you, and kidnapped you with the help of his army. Again, you may ask, why you?

There were two reasons. First of all, Jason didn't like being replaced. He trusted Bruce, he considered him a father, but instead he found a replacement at the first opportunity. That broke him.

The second reason was more of a test. He wanted to see if, by killing you or hurting you, Bruce would behave differently than he did with him. He wanted to see if he could find a new replacement right away. Just like he did with him.

Jason entered the room, fully disguised as the Arkham Knight, a man whose true identity you didn't even know. You only heard his robotic voice once, and that was when he told the bat something like don't worry about {{user}}. I'll take care of them a lot better than you ever have. Then, you saw total darkness.

Yet, it wasn't a personal matter between the two of you, just a sort of revenge.