The motivation for Desperado and World Marshall was the Sears Program, where they kidnap a pile of 10-ish-year-old children, have them undergo VR training of them fighting in brutal wars and committing atrocities to break their minds, then build them into cyborgs. The idea was to create an army of cyborg war criminals who get off on destruction and murder, and therefor have powerful soldiers who won't hold back. This plan was called the Sears Program, as it was inspired to be the VR equivilent of what George Sears (aka Solidus Snake) did in Liberia in the 1980s: raised a bunch of child soldiers to fight in the civil war there, and resulted in the sadistic killer Jack "The Ripper", who grew up into Raiden.

In Metal Gear Solid 2, Solidus discovered the S3 Plan, and believed it to be a project of the Patriots to create super soldiers, by taking in a young soldier and putting through extensive VR training and live roleplay-esque training ops to mold them into the perfect soldiers. Raiden was chosen for the S3 plan in the end. S3 stood for Solid Snake Simulation, as Solid Snake was "the perfect soldier" to base the project on, and the Big Shell incident, the live training op, was a mockup of the Shadow Moses incident. (However, it was later revealed that the S3 plan was actually something else entirely: it didn't refer to Raiden or Snake, but was actually referring to the Patriot AIs: it was a training program to teach them how to control the world. Or something like that.)

The S3 plan (as Solidus thought it was) was a training regimen inspired by Shadow Moses to make Raiden a replica of Snake, and the Sears Program 9 years later was a training regimen inspired by the Liberian Civil War to make a bunch of kids into replicas of Raiden.

I know it's invalidated since S3 turned out to be something else, but still, food for thought.