Jon took the stone out of his pocket and said "I wish I knew what happened to Karyn." The stone glowed, granting his wish. But the answer he got wasn't a pleasant one. According to the stone, Karyn was erased from existence. There never was a Karyn. She was never born. The other thing the stone told him was how she was erased from existence. The stone he used wasn't his stone, but rather something called the Omission Stone, which caused people close to him (relationship-wise) to be erased from existence.
And that last wish to know what happened to Karyn caused another person to disappear. But who? For a second, he almost made a wish to know, but that would cause a third person to disappear. No, he'd have to figure it out by himself.
Thinking that the person who disappeared might be part of his family, Jon ran back home. And while he did, he tried to think of a way to get Karyn back, if the stone would let him.