The player starts as a freelance space pilot in a shuttlecraft, out to make a penny in the vast and unforgiving galaxy. There are many ways to play Nova; for example, a starting player seeking funds can become a trader or courier, delivering cargo between worlds; become a pirate or bounty hunter, attacking and disabling ships to steal their money, cargo, or the ships themselves; become involved in one of the main storylines; or even conquer the galaxy by subjugating worlds.
The game has six major storylines that the player can participate in, one for each of the major factions: Federation, Rebellion, Auroran, Polaris, Vell-os, and Pirate.
These storylines are the bulk of the game. Each storyline is a long and involved set of plot-filled missions which are like "playing" a short story written in second person. Each story-line forces pilots to align themselves with a particular faction, restricting a player's freedom but giving him access to more powerful ships and technology. A single story-line can take anywhere from an hour to several days to play to completion, depending on the player's level of experience and preferred pace. There also exist a few shorter minor stories and missions, which are difficult to find but have great rewards, such as the ability to use the old hypergate system.