You will have to face two groups of levels, one after the other, in each of which there are three levels. You have the option to choose in which order to face the levels of each group, but only after completing all three can you move on to the next group. After completing all the levels of the second group you will access the final level, where you will finally meet Steelbeak. There are therefore seven levels in all.
You can access the various levels from the city map by selecting them with the Control Pad. For each level available, Launchpad McQuack will inform you about what is happening on the spot and ask you if he should accompany you there. At the end of each level you will have to face a member of F.O.W.L.. If you're looking for purely boss information, see the bosses page. After defeating the boss, you will return to the city map.