<p>Understanding interactions between rock and fluids is important for many applications including CO<sub>2</sub> storage in the subsurface. Today significant effort is aimed at research on CO<sub>2</sub> flow through low-permeable shale formations. In some experiments, CO<sub>2</sub> is injected in a shale sample at a constant rate, and the upstream pressure exhibits rise until a certain moment followed by a decline, representing the so called breakthrough phenomenon. After the breakthrough, downstream flux significantly rises. This behavior was thought to be the result of fracture occurence or mechanical effects.&#160;<br><br>Here, we present a 3D numerical model of flow through experiments in shale. Our model accounts for poroelastic compaction/decompaction of shale, its time-dependent permeability, and two-phase flow, the fluid phases being CO<sub>2</sub> and air. The model also accounts for a capillary entry pressure threshold observed in experiments. The key feature of the model are saturation-based relative permeabilities which result in sharp overall permeability increases as the CO<sub>2</sub> moves through the shale sample. The model is implemented for 3D calculations with the finite volume method. Our results show that CO<sub>2</sub> breakthrough is a natural outcome of two-phase fluid flow dynamics and does not need a fracture to exhibit pressure behavior observed in experiments.</p>