You would make an animation intro in the same way you would make anything on the screen move that isn't moved by the player.
You place items/objects and move them around using events - usually in some form of simple state machine - which are also used in making AI or other things that require controlled and evaluated flow.
Have you tried the ghost shooter tutorial in the Beginners Guide to get the basics of how C2 works yet? If not, it's highly recommended... if you already have done it, then you simply apply the same principles but for different reasons. It pays to think a little bit laterally when it comes to solving problems with event methodology.
To do something like a Boss jumping into the scene, you could have a trigger when the player gets to a certain point of the level, your state machine starts. At phase 1 you could disable control of the player (making it feel more cinematic) then start making dialog appear or objects create (like your boss). Phase 2 of your state machine might be the boss dropping from the ceiling to the floor and more dialog. Phase 3 might be the player regains control and the fight will begin.
Hopefully that made some sense?