Malcolm Colcord was a guard at the original Weapon X Project, a horrifically scarred survivor of Logan's escape from the facility. Years later, he petitioned for joint American / Canadian backing to restart the Weapon X Program as the new Director, manipulating mutants as black ops agents and test subjects for government purposes. He received his funding, and Weapon X was reborn.
The program suffered several setbacks and schisms over time, with Colcord and his second Brent Jackson locked in a struggle that divided Weapon X assets and agents between their two power bases. Other parties involved included John Sublime and the recently reactivated "parent" program, Weapon Plus, as well as Mister Sinister, who was using Weapon X's Neverland facility to cull test subjects for his experiments. The so-called "War of the Programs" was a secret conflict between these forces which suddenly ended on M-Day as nearly all the participants lost their powers in the Decimation. The aftermath was briefly seen in New Excalibur #9.
