At the end. The bartender tells Sam that he's (as in Sam), & always has been, in control of the leaps. He can go home anytime he wanted too. But there's so much out there that needs fixing that Sam realizes he can never go home. The bartender tells him "God bless you" for making this sacrifice and Sam leaps back to ...
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Sam's body, mind & soul made the leap. Before it would be just the mind & soul. His body would remain in the present day 1999 time chamber. When he leaped into a person's life. That person's mind & soul leaped back to Sam's body in 1999. In the finale, Sam's body goes missing which made it harder for Al & company to track him. So in the end. It seems that Sam can leap as himself to whenever without actually taking over a person's life. So of like Journeyman. Damn you NBC!
The finale airs next Wednesday on the Ion channel.