“The Ghost in the Machine” was directed by Milan Cheylov (one of 10 “Bones” episodes he helmed), who had to craft a distinct visual language. The episode is filmed almost entirely via POV shots from the perspective of Colin’s skull, with characters often speaking directly to the skull. To mimic a human’s point-of-view, the framing is imprecise and the camera sometimes shakes (presumably it was handheld). What is smooth are the pans; the camera moves on a 360-degree axis, changing view quickly like a wandering eye.
The episode does not unfold in real-time (there would be too much downtime to fit into 40 minutes). So, instead of simple cuts, transitions are done via plumes of ethereal smoke, which smog up the frame and then disappear to reveal the new location. Hanson admitted to THR that the concept wasn’t easy to execute: “[Executive producer Stephen Nathan] had a hard time cutting it, and [Cheylov and his crew] had a tough time shooting it. I painted myself into quite a stylistic corner. Everybody had to help me out.”
As a sign that Hanson ultimately needed to escape that corner to resolve the episode, his script only stays confined to the lab for the first two-thirds of the episode. In the last 15 minutes, Bones brings the skull home, convinced Colin’s “presence” will motivate her to see the case through. Then, when they’ve got the suspects pinned, we see the questioning and confession thanks to the skull being in the room as an interrogation tactic.