The Colonel is debatably the true antagonist in the video game; Metal Gear Solid 2: Sons of Liberty. He's a computer AI that was created by GW, that took the form, as well as the voice of Colonel Roy Campbell, and is a member of the Patriots. He first serves as Raiden's guide during the Big Shell Incident, but then becomes Raiden's enemy after he found out the Colonel's secret.
Big Shell Incident
The Colonel was originally served as a guide for Raiden during the Big Shell Incident. Most of the time, The Colonel would give Raiden information about the "terrorists", and give him specific direction on how to complete the mission. But as Raiden's mission progressed further and further, The Colonel began to act rather strangely, as he kept calling Raiden's mission a simulation when Iroquois Pliskin, aka, Solid Snake arrived on the Big Shell to assist Raiden.
Super Smash Bros Brawl
Though the Colonel doesn't appear as a playable character in Super Smash Bros Brawl, he does appear as one of Snake's taunts, though only when calling while fighting Luigi (to which he insults Luigi by calling him the King of Second Banana), where he is implied to have replaced Roy Campbell during that instance.
At first the Colonel had roughly the same personality as Roy Campbell's, but as the game progressed he's started to show signs of being an AI. After Raiden found out the Colonel was an AI, the Colonel's personality changed.
Metal Gear Solid: Portable Ops
Metal Gear Solid: Peace Walker
Metal Gear Solid V: Ground Zeroes
Metal Gear Solid V: The Phantom Pain
Metal Gear 2: Solid Snake
Metal Gear Solid
Metal Gear Solid 2: Sons of the Liberty
Metal Gear Solid 4: Guns of the Patriots
Metal Gear Rising: Revengeance