If there was a massive pandemic Commander Shepard would stay inside his ship with his crew for the majority of the time to not risk spreading the disease. Since Shepard is part cyborg he cannot get the virus. There is quite a lot to do on the ship hell they could even leave the planet for a few weeks until they can come back. Despite that Shepard would spend time in the simulations working on his defensive game. Shepard would also catch up with his best friend Garrus. They had a few binging nights talking about the good ol days of saving the galaxy. He also had Grunt keep him in peak physical shape practing some sparring and head buts. After all that Shepard would volunteer at the local Winnipeg hospital helping out where he can in his space suit to insure no contamination. Shepard also brought EDI with him and the AI worked tirelessly to find a cure.