It was the episode where Sayid takes the new guy they find, the put him in the hatch and Sayid tortures him. At one point John and the doctor start fighting over the dude being tortured and the doctor let's the time on the clock run out. John comes in at the very last second and resets the timer.
Now as of the last episode, John and the doctor aren't getting along well. The prisoner is impanting messages into john that the doctor is the one calling all the shots on the island, and it has John livid.
Who is this prisoner!
XI Wiki

