New forms of carbon-based materials have received great attention, and the developed materials have found many applications in nanotechnology. Interesting novel carbon structures include the carbon peapods, which are comprised of fullerenes encapsulated within carbon nanotubes. Peapod-like nanostructures have been successfully synthesized, and have been used in optical modulation devices, transistors, solar cells, and in other devices. However, the mechanical properties of these structures are not completely elucidated. In this work, we investigated, using fully atomistic molecular dynamics simulations, the deformation of carbon peapods under high-strain rate conditions, which are achieved by shooting the peapods at ultrasonic velocities against a rigid substrate. Our results show that carbon peapods experience large deformation at impact, and undergo multiple fracture pathways, depending primarily on the relative orientation between the peapod and the substrate, and the impact velocity. Observed outcomes include fullerene ejection, carbon nanotube fracture, fullerene, and nanotube coalescence, as well as the formation of amorphous carbon structures.