The explanation was strange, but no stranger than the idea of magic stones in the first place. Liz and Jennifer were from a parallel universe. Jennifer was the Jon of that parallel universe--she even had her own stone, but she was female and lived in California with her aunt and uncle after her parents had died in an accident.
Jennifer wished for things to be different. This wish threw Liz and Jennifer into different universes. Liz fell into Jon's universe; Jennifer was lost.
Liz had previously wished for the power to keep track of Jennifer. This power instead homed in on Jon, since Jon was this universe's version of Jennifer. So Liz came to Indiana to find Jon.
"So now you know," said Jon.
"Oh, god, I'm sorry," said Liz. "I really screwed this up. You're not Jennifer. That's why the stone seemed to move you from California to Indiana even though it was outside the stone's range--you were in Indiana all along. That stone never touched you! And I bet there are counterparts of everyone--another me here, another Karyn in my world--but we're in different states, so we never met."
"Look," said Jon, "it's okay. You had no way to know. You didn't have a stone to ask."
"I could have just asked the stone the moment I got it instead of putting you all through this trouble."
"I have an idea," said Karyn. "Jon, we could help Liz. You have your stone. Let's find Liz's friend. Jennifer really is lost, after all. Besides, she's a parallel universe version of you--you would help yourself, right?
"Would you really do that?" asked Liz.
"I don't know..." said Jon. But he knew just how much trouble the stone could cause. Would he refuse to help someone who was a lot like himself and had worse stone trouble? "I... Yeah, Karyn and I will help you. I wish that me, Karyn, and Liz would travel to the universe that Jennifer went to."
Things shimmered around them. It looked like they were still in Jon's house, but things were slightly different--a different colored carpet, an umbrella rack moved a foot away. A parallel universe, with things almost the same, but not quite.
"Watch it," said Karyn. "I've seen those sci-fi shows. We could be in trouble!"
"But it's still my house," said Jon.
"Jon," explained Karyn, "There could be versions of anyone we know here. It all depends on where we go. If we go to California, there might be another Liz, unless she moved. If we stay here, there might be another you and me and Sarah, unless they moved. And that doesn't count Jennifer, who's also another you."
"I'm worried that something happened to Jennifer," said Liz. "She didn't come back to get me. For all I know she came to Indiana just to see her parents alive again and this universe's Jennifer or Jon or whoever, stole the stone from her."
Jon said, "Or maybe this universe's me already has their own stone. There could be three people walking around with stones here--me, Jennifer, and this other person. Anyway, Liz, you said you had the power to keep track of Jennifer. We're in the right universe to find her--can you use that power now?"
Liz concentrated a moment and then said, "Jennifer is...."