Totally Spies! 2: Undercover is broken up into five episodic missions. Each one has the three girls, Clover, Alex and Sam, hunting down and capturing one of their main enemies. Along the way, Jerry will give you various tools and you will run into friends like Arnold.
The missions will not only have you facing off against enemies like Geraldine, but also Kyle, Broccoli-Boy and Carrot-Man. Episodes are action/adventure like levels with interesting puzzles slipped in between. For instance, the first mission I took on (there are multiple opened at the beginning), was Arnold the Great. First you had to race down a busy street to catch up to and scan a stolen armored truck. After that, you have to break into the truck by shorting out the circuitry on the lock; this is done by connecting specific diodes with the stylus while avoiding various obstacles with the stylus.
At the end of each mission, the spies will debrief you and ask you a series of questions. These are things like "How many times did you have to scan the truck" or "How many diodes did you have to connect". If you answer all the questions correctly, you will unlock a gallery of the images used in that mission.
Each of the mini-games you get past in Undercover can be played in multiplayer mode. These are basically just playing through the mini-game again but now you have your friend's progress bar visible too.