This was a PC game from the early to mid 2000s. I believe it was between 2002 and 2006. It was an indie title, as far as I'm aware.

The game itself was a god game like Black & White, Populous, or I suppose Dungeon Keeper. The setting was a virtual world with graphics inspire by vector line games or Tron. Monstrous enemies were all basic three dimensional models, but the units in the player's army were all represented by identical two dimensional sprites of stick men. Similarly, enemy "gods" were represented by the same sprites. You (generally) did not have direct control of any units, but under certain circumstances you could control them. I recall being able to manually control turrets that your units had captured, for example. There were some "spells" similar to how Populous works.

The story that connected the series of levels was of you guiding these sentient or semi-sentient "programs" (your units) in preventing the system from being overtaken by some viral outbreak. The story was all told in text.