Depending on the location, the player controls one of two characters. During gameplay the world is observed from the first person perspective and all its elements are fully rendered in 3D. Diverse and interesting puzzles are the greatest strength of the game. Their difficulty increases as the plot progresses. Nemezis features logic puzzles, jigsaws, codes with complex mechanics, and associative riddles. There’s also a new type: spatial puzzles. In order to solve one the player has to reach every element of the puzzle and study them closely.

Game features two puzzle difficulty levels, which should make the game appealing not only to players expecting great intellectual challenges, but also to those who mainly want to experience a fascinating story. The player may carefully search every in-game location, in order to solve riddles. He may also use the advice of an electronic guide, commenting on the player's efforts and giving him tips (after some time it turns out that the guide is becoming increasingly unpredictable and some of its advice may lead the player astray).

We pay great attention to balancing the gameplay and making its consecutive challenges intuitive. On the one hand the player is being challenged and on the other draws satisfaction from every step of the progress. As the story moves on, the player learns a growing portion of the mechanics, so becomes better at the game and notices progress. The game is easy to learn, but exploring it fully by playing on Hard mode is reserved for the most demanding players.