At the start when they appear, they started to shoot their machine guns at her. While the Helicopters are shooting at her, Noodle takes refuge in the windmill. The helicopters then continue to fire at the windmill and damage it.
Later in the video, the helecopters damaged the floating island while it fell to the Earth. One of the helicopters drops a bomb on the island, so they can say that they have killed Noodle for sure, in case they thought if she was still inside the windmill and survived the crash.
But they were fooled when they didn't realize that Noodle was parachuting way above them.