This work investigates the interplay of gas transport in the microcracks and matrix of shale using He and CO2 via transient upstream pressure-pulse-decay experiments. The microcracks are natural in the sense no laboratory pretreatment created them. A novel setup of the pressure-pulse-decay experiment was used to determine the storage and flow capacities simultaneously. Experimentally, the pressure signals are used to define time-dependent pore volume partitioning between the microcracks and the matrix. A dual continuum simulator is constructed to decouple the flow and storage capacities at early time where the gas flows simultaneously in both media. A history-matching process quantifies the pore volume partitioning of the microcracks and matrix, the permeability in the microcracks, and the diffusivity of gas in the matrix. A series of experiments were conducted on four shale samples from Eagle Ford and Haynesville shale plays at constant net effective stress of 500 psi and at increasing net effective stresses of 500, 1000, and 2000 psi. Results show that the pore volume of the microcracks in sample 180Ha (Eagle Ford) was from 8.0 to 24.1% of the total pore volume in all experiments at constant and variable net effective stresses. The Haynesville samples (TWG 1-3 & 3-3) had between 68.9 and 87.0% of the total porosity in the microcracks while the remaining percentage represents the pore volume in the matrix. These proportions are related to the magnitude of permeability and void volumes in the system. The values of Klinkenberg-corrected permeability estimated using He vary between 396 and 1.6 D. The role of adsorption was also investigated using CO2 in the same experimental apparatus and conditions. It was found that the influence of pore volume partitioning is suppressed by the large adsorption capacity in the shale samples. It was found that adsorption occurs in the microcracks in permeabilities less than 50 D along with adsorption in the matrix. For permeabilities greater than that value, adsorption had no importance on microcracks. Adsorption in both media required different adsorption-pressure functions. The CO2 permeability was found to be smaller than the He permeability by 2-3 factors. CO2 injection into the core caused a reduction in permeability that was observed with He injection after CO2 flooding. The He permeability dropped by a factor of 2-3. This permeability hysteresis is attributed to the reduction in pore size accessed by the gas. This observation provides another reason why CO2 storage in depleted shale gas reservoirs is practical. Reduction in gas permeability may be essential to keep CO2 underground for as long as possible.