A scene (implemented with the CCScene object) is more or less an independent piece of the app workflow. Some people may call them “screens” or “stages”. Your app can have many scenes, but only one of them is active at a given time.

For example, you could have a game with the following scenes: Intro, Menu, Level 1, Cutscene 1, Level 2, Winning cutscene, losing cutscene, High scores screen.

You can define every one of these scenes more or less as separate apps; there is a bit of glue between them containing the logic for connecting scenes (the intro goes to the menu when interrupted or finishing, Level 1 can lead you to the cutscene 1 if finished or to the losing cutscene if you lose, etc.).

A cocos2d CCScene is composed of one or more layers (implemented with the CCLayer object), all of them piled up. Layers give the scene an appearance and behavior; the normal use case is to just make instances of Scene with the layers that you want.

There is also a family of CCScene classes called transitions (implemented with the CCTransitionScene object) which allow you to make transitions between two scenes (fade out/in, slide from a side, etc).

Since scenes are subclasses of CCNode, they can be transformed manually or by using actions. See Actions for more detail about actions.