Johnny Test begins with Johnny meddling in his twin sisters' lab. It's all an attempt to get his video games to work on their fancy simulator, which ends up opening it up to other nefarious villains. Johnny knows his parents would be really mad if they found out, so he goes into the simulator to stop the villians and set things right again.
Each level features a different alter-ego of Johnny, with the first being regular Johnny, the next being Johnny X, a superhero form of himself, and so on. Each form has a different special power you can unlock. Johnny has a super jump that will get him to inaccessible points on the map, and that's generally how it goes. You need to melt ice blocks in the second level, so you'll get a fire blasting power to help you do that.
That's basically all there is to this game. The cut-scenes between levels are rather amusing, and feature the banter between Johnny, his sisters, villians, and his dog. These are the parts of the game that feature the art style from the cartoon as well, and they look a lot better than the playable game. It's kind of a shame that the gameplay couldn't feature the highly stylized art from the cartoon. It just barely hints at it in the backgrounds.
