There are two kinds of Cryptoku games: Crypto and Hack.
In the Crypto game, your goal is to get through all 50 levels. If you get 50 intrusions on one level, the game ends... but you can retry that level.
Hack is a sudden-death game; when you get 10 intrusions, the game ends (there's no retry). Hazards appear earlier than in Crypto games, and Hack games start with a 3x3 grid.
In both game types, you can earn bonus points by completing a level with zero intrusions.