I'm pretty sure there was a Voyager episode where Tom Paris (and another officer) were playing a real-time strategy game (like Age of Empires) but then they found out they are controlling actual dueling civilizations.
I suspect you are getting Voyager confused with an episode of Stargate Atlantis.
The Season 3, Episode 15, The Game had the same premise, with McKay and Sheppard finding and playing what they believe to be a computer game left behind by the Ancients. Only to discover that they are actually sending commands to two different countries and civilisations on an actual planet, causing conflict between them.
Major Lorne's team discovers a planet that fits the description of what Sheppard and McKay mistook as a video game they found in the Atlantis database. It turns out that, through a series of Ancient satellites above planet M4D-058, the game has been controlling real people, the People of Geldar and Hallona, who now stand on the brink of war and destruction.