The 'Virtual 'Icon of Sin is the last boss of Doom II RPG towards the end of the game. He takes ontrol of a machine that greatly resembles the Icon Of Sin. While the Virtual Icon Of Sin is technically a different entity than the normal Icon Of Sin, the two are verry similar.
As the Icon of Sin turns to rubble and dust, the evil presence you've felt dissipates. Though VIOS has been destroyed, you sense that elsewhere other battles are raging. You may have won this battle, but the outcome of this WAR has yet to be decided.
Behind the scenes
The nods to 'other battles raging' and "WAR has yet to be decided" is likely a reference to Doom I and Doom II, Final Doom, and Doom 64. Though this may not be the case as Doom 2 RPG's place in the timeline is uknown (other than being after Doom RPG).