Clark and his colleagues become suspicious about the spate of major terrorist attacks occurring within a few weeks. Unbeknownst to them, the attacks are part of an intricate conspiracy to wipe out nearly all of humanity, codenamed "the Project". Dr. John Brightling, a staunch radical environmentalist who heads a biotechnology firm called the Horizon Corporation, ordered the attacks through ex-KGB officer Dmitriy Popov to raise fears of terrorism, allowing co-conspirator Bill Henriksen's security firm to secure a key contract for the Olympic Games in Sydney, Australia. Henriksen would then ensure the release of "Shiva"—a manmade Ebola biological agent more deadly than the one that spread a year prior, developed by Horizon and tested on kidnapped human test subjects—through the fog-cooling system of Stadium Australia, infecting everyone present, who would spread Shiva after returning to their home countries. The resulting pandemic would kill countless people, during which Horizon would distribute a "vaccine"—actually a slow-acting version of Shiva—ensuring the deaths of the rest of the world's population. Brightling's "chosen few", having been inoculated with the real vaccine, would then inherit the emptied world, justifying their genocidal actions as "saving the world" from environmentally-destructive human society.

The Sheva Strain was a viral pathogen that was developed by the Weapon X Program and used by Professor Truett Hudson on the test subjects at the facility. The aim of the project was the creation of supersoldiers from Mutants that possessed a healing factor. This strain was cultivated to serve as a failsafe by the Program to better control their subjects. The Sheva Strain was highly adaptable and lethal with it being capable of killing a normal Human in a single year. It was in use by 1968 where it was introduced into the body of Wolverine when he was abducted by the Program for Experiment X. When Logan managed to escape, he confronted the Professor with the intention of killing him whereupon Hudson revealed that all Weapon X subjects were implanted with a dormant deadly virus in the form of the Sheva Strain.

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.