Underground CO2 storage is a key strategy to achieving net-zero targets by 2050, which requires gigatonne-scale containment of gaseous CO2 in geological formations. Shale rocks play a role in both trapping CO2 and preventing its escape, thus ensuring containment security. However, shale integrity can be compromised upon interaction with CO2, which should be carefully evaluated. This study explores the dynamic behaviour of CO2- shale interaction at the pore scale, focusing on the physiochemical interactions between CO2 and shale, including the impact of shale swelling, where CO2 adsorption causes matrix deformation and alters fracture sizes. Here, we utilise image-based analyses to develop a triple-porosity pore network model (PNM), reflecting the complex nano- to micro-scale structure of shale, to examine CO2 injection into methane-saturated environments. The study particularly focuses on the impact of matrix deformation caused by gas sorption (swelling), competing with mechanical stress effects. Findings indicate that CO2 injection leads to a reduction in fracture permeability by up to 17 % and 10 % in low- and high-density fractured shales, respectively, under high confining pressure (50 MPa), and by 15.5 % and 8 % under lower confining pressure (25 MPa). Although fracture permeability versus CO2 injection pressure reduces monotonically at the lower confining pressure, that of the higher confining pressure is non-monotonic, where the fracture permeability shows an increase due to effective stress change. Additionally, the average fracture aperture size decreases by 50 nm in low-density and 25 nm in high-density fractured shales, highlighting the critical balance between swelling effects and mechanical stresses in the geological sequestration of CO2.