Metal Gear Solid Philanthropy/WMG

The soldier Snake spared in the opening is either Black Arts Viper or the Fiend of Kalcabar.

 * Chekhov's Gunman, anyone?

Nanomachines are responsible for the Overnight Nation.

 * The very end of the opening titles sequence seems to suggest this, with imagry evocative of electronics or networking, finally zooming in on a sphere that reads " V.4.5.10.1." During the film, Harrison mentions that the Overnight Nation acts "In the name of Jubal." They shout "Jubal!" as a battlecry and behave almost like zombies. Vitalij, a native of the area, is perfectly normal until he sees the complex where the fighting is taking place, and there is clearly a process of some kind that turns him nuts. Brainwashing via nanomachines would explain everything.

Abraham Bishop works for the Patriots.

 * To what end, who knows, but one of the film's trailers does mention the Patriots, so the film's continuity may very well include them.