After the stone glowed for a second time, Jon's eyes went wide with shock. His grandfather's wish was:
I wish I had a grandson named Jon.
Jon didn't know how to react. He was just finding out that he wasn't supposed to exist! Did that mean that he wasn't real? He figured that his grandfather would make a lot of wishes, but he had no idea that he would do something like this.
Now since Jon knew the truth, he began to wonder what that reality was like, the one in which he didn't exist. He was glad that his grandfather's wish prevented him from removing himself from this reality, of course, but still ... he just didn't think it was right for that reality to be totally forgotten.