In Protein Purge, players take on the role of a rogue scientist on a mission to clear dangerous misfolded proteins from the nuclear and cytoplasmic inclusions of infected cells. With limited resources, players must navigate a variety of different levels and obstacles to find the "garbage dump" site and send the misfolded proteins to the vacuole for degradation. Along the way, players will encounter a variety of different enemies, including rival scientists and security forces, all looking to stop them from achieving their goal. Players must utilize a combination of strategy, stealth, and combat to overcome these challenges and save humanity from these deadly proteins.