Here's how you get it:
1. Beat the Elite Four and become the Champion. This will trigger the post-game story.
2. Talk to Professor Oak in New Bark Town. He'll tell you about a new threat in the Kanto region.
3. Head to the Viridian Forest. Follow the path to the west of the gym, and you'll find the entrance to the forest.
4. Go through the Viridian Forest and defeat the trainers you encounter.
5. Head to the Indigo Plateau. This is the location of the Kanto Elite Four.
6. Talk to the person standing near the entrance of the Indigo Plateau. They will give you HM Waterfall.
Remember that you'll need a Pokemon that knows Cut to get to the Viridian Forest after the main game is completed.