Neo includes several major and minor changes. The game does not feature traditional Terrorist versus Counter-Terrorist scenarios, the two sides are renamed CSF and NEO respectively. It incorporates a matchmaking and Elo-derived rating system to help keep players and teams on even footing. The game is anime-styled to better market it in Japan.

Along with Neo, there are several Flash visual novels spin-offs set within the same setting made by developer Romancework, titled Counter-Strike NEO -WHITE MEMORIES-. The visual novels have a continuing storyline and even some portions that loosely resemble Counter-Strike gameplay.