Footage from MGS: VR Missions is shown several times, such as when Raiden's telling Pliskin about his VR experience or when the "Crazy Colonel" is going nuts in Arsenal, mentioning many of the VR missions. Also, the end credits say that footage from this game is in it.
Several references are made to MGS: VR Missions. Raiden and the Colonel mention several specific missions (such as Variety Level 7, Variety Level 13, and Advanced Level 4). Also, the open space where Raiden fights the Metal Gear RAYs has the same holographic hexagonal floor featured in the "Photography Mode" in VR Missions.