Shades of Niels Bohr and Werner Heisinger! "The Atom" - aka Yonko's Proof - is a representation by John Yonko of the entire process - from God's first thoughts about creating 'something' (back when there was no thing) to the actual creation - of the first atom. The movie begins with amorphous blobs and waves of immaterial thought that occur in God's mind before they are refined into the design of the actual first atom of creation.
At this point - I say point because there was no time at that time - the blobs and waves of thought constitute the first example of particle/wave theory. Appaarently, what happened was that, at the pre-moment of creation, God observed His own wave of thought (which we might refer to as the original or first Kopenhagener Geist), causing it to collapse into the particle we now refer to as an atom. If the Copenhagen Interpretation is indeed correct - that an observation by an observer collapses a wave into some"thing" we call a "particle" , then "The Atom" offers an orchestrated visualization of a Quantum Mechanical proof of the existence of God - the First Observer. Or perhaps not. That's the beauty of Quantum Theory: everything is a probability, but not necessarily a reality. And, while "The Atom" may portray the thought or thoughts that became the wave or waves that became the atom or atoms, it doesn't begin to asnwer the question"why?".
"We'll have to deal with that in another video", says Yonko.