Fly By Dire" is an orchestral piece from the Season 6 soundtrack. It plays during the finale.
The title of the song is a reference to a fly-by-wire system in an aircraft. Traditional aircraft systems are controlled by physical means: the pilot moves the flight controls, which subsequently moves physical components, such as cables, rods, or pulleys and creates movement in the correct place on the aircraft. Fly-by-wire, typically used in larger aircraft, instead replaces these physical means with electronic impulses for the ease of flight and maintenance. This title indicates that Sawyer is such a system, delivering a "dire" message from one source (the MiB) to another (Jack).