We present the Illustrated AlphaFold, a visual walkthrough of the architecture and information flow of AlphaFold 3. We explain every model component and training detail, with particular focus on the advances since AlphaFold 2 – including the unified tokenization scheme that extends to DNA, RNA, and small molecules, as well as the novel diffusion-based structural module. Finally, we include some musings on the ML lessons learned from studying AlphaFold 3.