My friend says I am crazy for seeing anything in this video, but here goes...
I think the whole video is a story of Jesus, or some other religious figure (the stars within the apple is a symbol of three religions to me). The human in the video represents all humanity and its history. The human touches a tree of knowledge, his brain expands, he sees the forest for the first time... All the while, science (the baloon figures in the form of a multiplying cell/atom) is growing. Jesus, the clay man, is always with the human. When the human ignores the clayman, science kills the clayman. The human mourns and examines the clayman. He ventures into the forest (growing knowledge) only to be hunted by science. He is only saved by opening his Third Eye, escaping the Shadow form that science has taken.
Pretty good interpretation and yes the symbols in the apples have something to do with religion. They are symbols of Chakras.
Although I don't know if this isn't what you mean or not, but are you saying he gains his third eye so that he can find religion again? It's quite the opposite cos gaining a third eye means thinking for yourself basically.
