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. Our 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 jumbo phage build a compartment that compartmentalizes its replicating genome to avoid host defenses that acts akin to a eukaryotic nucleus.