The mysterious intruder did not sneak into Zoe's room at night to replace the wishing stone with a similar (but different in its rules) stone, but it was not for lack of trying. The intruder snuck into the household, but found himself unable to enter Zoe's room, as if an invisible barrier barred his way.
Wards! The girl has magical wards around her room, the intruder realized. Indeed, the intruder could not enter Zoe's room via the window or the door, or in fact in any way. The intruder therefore had no option other than to leave and hope to find an opportunity later to switch the stone. Zoe most likely wouldn't keep the stone in that room for good. She'd likely take it with her to school, or just outside. There'd be opportunities for a switch later.
So the intruder left the Gibson house without the wishing stone and still carrying the stone he'd intended to switch with the wishing stone, and Zoe awoke.
As described in the previous episode, Zoe grabbed her book bag and more importantly, the wishing stone, before heading off to school. She had shown the stone to her best friend Athena the previous day, but hadn't had a chance to make some serious wishes. Today was the day that she would. And she wanted to make sure her friend was around so that her memories wouldn't change along with everyone else's.
It was, in fact, Zoe's friend Athena who had placed the magical wards on Zoe's room preventing any strangers from entering it. Athena DeVries was the biggest expert on magic that Zoe knew, so Zoe was sure Athena would be very interested in a stone that magically altered reality when someone made wishes. Athena had already expressed an interest in seeing just what the stone was really capable of.
The mysterious intruder, meanwhile, knew very well what the stone was capable of. And he knew all too well what the other stone he carried - the one he intended to switch with the regular wishing stone - was capable of. So he would secretly follow Zoe and find another opportunity to switch the stones.
But which stone did the intruder have, and why did he want to switch this stone with the regular wishing stone?
