The Last of Us begins in a Boston quarantine zone 20 years after a fungal plague called Cordyseps Unilateralis decimated modern civilization. Ellie, a 14 year old orphan lives in a strict boarding house, and Joel, who is a black market dealer within the quarantine zone sells weapons and drugs.
An event occurs when Joel makes a promise to a dying friend that he will protect Ellie and help her escape. As they both make their way out of the quarantine zone with their lives, the game then starts to play throughout areas across the United States.
Evidently, things take a turn for the worse, as the military quickly finds out about their escape and begins pursuing them.