Code Yellow is a pre-programmed trigger phrase used to control Jack by Frank Fontaine. Rather than triggering direct action, as the "Would you kindly" trigger phrase did, this one triggers autonomic processes, specifically directing the subject's heart to stop beating. This doesn't happen immediately; as Fontaine notes, "The heart's a stubborn muscle, but it ain't that stubborn." The result is a series of periodic spasms that reduce Jack's maximum health, weakening him greatly over time. Fontaine uses this phrase in an attempt to eliminate Jack upon discovering that Dr. Tenenbaum had disabled the "Would you kindly" trigger.
Jack eventually frees himself from this (and any other triggers that may have remained) by consuming two doses of Lot 192, thus restoring his maximum health to its previous state and freeing his mind once and for all.