To perform their function, biological systems need to operate across multiple scales. Current techniques in structural and cellular biology lack either the resolution or the context to observe the structure of individual biomolecules in their natural environment, and are often hindered by artifacts. My lab’s goal is to build tools that can reveal molecular structures in their native cellular environment using the power of cryo-electron tomography to image biomolecules at molecular resolution in situ. I will show how we used these techniques to discover how we characterized a new family of phage, chimalliviruses, that build a sequence of compartments, primarily membrane- or protein-based, that protect the replicating genomes from host defenses while functioning akin to eukaryotic nuclei.