Gideon realizes he is missing one final key (the Creation Key ) to fully merge the worlds. To find it, he kidnaps Jamie and shoots Josh (who survives the wound) to force information out of them.
'Locke & Key' Season 3, Episode 6 Recap: 'Free Bird' - Vulture [S3E6] Free Bird
After assisting Bode, Sam’s ghost manages to jump into the unoccupied body of Gideon's henchman, James Bolton , effectively returning to the physical world to help the Lockes. Gideon realizes he is missing one final key