Amount of natural gas contained in the gas hydrate accumulations is twice that of all fossil fuel reserves currently available worldwide. The conventional oil and gas recovery technologies are not really suitable to gas hydrates because of their serious repercussions on geo-mechanical stability and seabed ecosystem. To address this challenge, the concept of methane-carbon dioxide (CH4-CO2) swapping has appeared. It has the potential in achieving safe and efficient recovery of natural gas, and sequestration of CO2. By this way, the energy generation from gas hydrates can become carbon neutral. This swapping phenomenon has not yet been elucidated at fundamental level. This work proposes a theoretical formulation to understand the physical insight into the transient swapping between natural gas and CO2 occurred under deep seabed and in permafrost. Addressing several practical concerns makes the model formulation novel and generalized enough in explaining the swapping phenomena at diverse geological conditions.