In his mad dash to leave his room, Jon accidentally bumped into his little brother Mikey and immediately swapped bodies with him, meaning that his "essence" hopped into his brother's body.
"Mikey, watch where you're going," Jon saw his body say, and then watched as it briskly walked down the hall and down the stairs, leaving Jon to stand in the hallway.
He looked down at himself and saw that he was in Mikey's body. "Weird," he said, noticing that he also had Mikey's voice.
Now, if Jon was in Mikey's body, then who was in Jon's? In the story, Charlie started out as someone else and not himself. But it seemed like in this case that Jon's body was Jon, mentally. Almost as if a copy of Jon was made and was forced to move into Mikey's body.
Wanting to see what the "left-over" Jon was up to, he decided to follow him.