What do I do in the air realm?

Try shooting the cannon.

As you might have guessed, your goal has something to do with the tornado.

When you first enter this realm, you probably won't have much luck hitting
the tornado -- it's too good at avoiding the red beam the cannon shoots out.

But that's only because you haven't set the cannon properly.

Have you tried looking down from this screen?

Look through the pipe and you'll see some balls on a grid.  These balls
control how the cannon shoots.

The cannon can shoot up to 9 beams, in a pattern determined by how the balls
are arranged on the squares in the center of the grid.

In other words, if there's a ball in one of those nine squares, the cannon
will shoot out a beam in the same place on a 3x3 grid.

You actually don't want to hit the tornado itself.

All you want to do is trap it.

Which means you need to put balls on all of the center 9 squares except the
one in the very middle.

You can move the balls with the controls on the sides of the box.  Each
control pushes the balls away from the control -- for example, the knobs at
the top slide all of the balls in that column down one square.

And you can freely move the balls along the very outside of the box, because
it doesn't matter how you position the balls there in the long run.  Use the
controls along the very top and bottom and sides of the box to get everything
into position, and then use the center controls only when you're ready to put
the balls down in their final positions.