In 2013, an outbreak of a mutant Cordyceps fungus ravages the United States, transforming its human hosts into aggressive creatures known as the Infected. In the suburbs of Austin, Texas, Joel (Troy Baker) flees the chaos with his brother Tommy (Jeffrey Pierce) and daughter Sarah (Hana Hayes). As they flee, Sarah is shot by a soldier and dies in Joel's arms.
Twenty years later, civilization has been decimated by the infection. Survivors live in heavily policed quarantine zones, independent settlements, and nomadic groups. Joel works as a smuggler with his partner Tess (Annie Wersching) in the quarantine zone in the North End of Boston, Massachusetts. They hunt down Robert (Robin Atkin Downes), a black-market dealer, to recover a stolen weapons cache. Before Tess kills him, Robert reveals that he traded the cache with the Fireflies, a rebel militia opposing the quarantine zone authorities. The leader of the Fireflies, Marlene (Merle Dandridge), promises to double their cache in return for smuggling a teenage girl, Ellie (Ashley Johnson), to Fireflies hiding in the Massachusetts State House outside the quarantine zone. Joel, Tess, and Ellie sneak out in the night, but after an encounter with a government patrol, they discover Ellie is infected. Full infection normally occurs in under two days, but Ellie claims she was infected three weeks earlier and that her immunity may lead to a cure. The trio make their way to their destination through hordes of the infected, but find that the Fireflies there have been killed. Tess reveals she has been bitten by an infected and, believing in Ellie's importance, sacrifices herself against pursuing soldiers so Joel and Ellie can escape. Joel decides to find Tommy, a former Firefly, in the hope that he can locate the remaining.
With the help of Bill (W. Earl Brown), a smuggler and survivalist who owes Joel a favor, they acquire a working vehicle from Bill's neighborhood. Driving into Pittsburgh, Pennsylvania, Joel and Ellie are ambushed by bandits and their car is wrecked. They ally with two brothers, Henry (Brandon Scott) and Sam (Nadji Jeter). After they escape the city, Sam is bitten but hides it from the group. As his infection takes hold, Sam attacks Ellie, but Henry shoots him dead and commits suicide. In the fall, Joel and Ellie finally find Tommy in Jackson, Wyoming, where he has assembled a fortified settlement near a hydroelectric dam with his wife Maria (Ashley Scott). Joel decides to leave Ellie with Tommy, but after she confronts him about Sarah, he lets her stay with him. Tommy directs them to a Fireflies enclave at the University of Eastern Colorado. They find the university abandoned, but learn that the Fireflies have moved to a hospital in Salt Lake City, Utah. The two are attacked by bandits, and Joel is severely wounded while escaping.
During the winter, Ellie and Joel shelter in the mountains. Joel is on the brink of death and relies on Ellie to care for him. Hunting for food, Ellie encounters David (Nolan North) and James (Reuben Langdon), scavengers willing to trade medicine for food. David turns hostile after revealing the university bandits were part of his group. Ellie manages to lead David's group away from Joel, but is captured; David intends to recruit her into his cannibal group. Refusing, she escapes after killing James, but David corners her in a burning restaurant. Meanwhile, Joel recovers from his wounds and sets out to find Ellie. He reaches her just as she kills David with a machete, an act which traumatizes her, and comforts her before they flee.
In the spring, Joel and Ellie arrive in Salt Lake City. Ellie is rendered unconscious after almost drowning, before they are captured by a Firefly patrol. In the hospital, Marlene tells Joel that Ellie is being prepared for surgery: in hope of producing a vaccine for the infection, the Fireflies must remove the infected portion of Ellie's brain, which will kill her. Unwilling to let Ellie die, Joel battles his way to the operating room, kills the lead surgeon, and carries the unconscious Ellie to the parking garage. He is confronted by Marlene, whom he shoots and kills to prevent the Fireflies from pursuing them. On the drive out of the city, when Ellie wakes up, Joel claims that the Fireflies had found many other immune people but were unable to create a cure, and that they have stopped trying. On the outskirts of Tommy's settlement, Ellie expresses her survivor guilt. At her insistence, Joel swears his story about the Fireflies is true.
After the events of the first game, Joel Miller (Troy Baker) confesses to his brother Tommy (Jeffrey Pierce) his responsibility in preventing the Fireflies attempting to find a cure for the Cordyceps fungus pandemic by saving Ellie (Ashley Johnson). Four years later, Joel and Ellie have built a life in Jackson, Wyoming, though their relationship has become strained. While on patrol, Joel and Tommy rescue a stranger, Abby Anderson (Laura Bailey), from an Infected horde. They return to an outpost run by Abby's group, former Fireflies who are now part of the Washington Liberation Front (WLF), a militia group based in Seattle, Washington. They attack Joel and Tommy; Abby seeks revenge against Joel for murdering her father, a Firefly surgeon (Derek Phillips). Meanwhile, Ellie and her girlfriend Dina (Shannon Woodward) leave Jackson in search of the brothers. Ellie enters the WLF camp to witness Abby beat Joel to death, and swears revenge.
Tommy sets out for Seattle to hunt Abby, and Ellie and Dina follow him. After escaping a WLF ambush, Ellie reveals her immunity to Dina, who in turn reveals she is pregnant. The next day, Ellie pursues Tommy alone and encounters Jesse (Stephen Chang), Dina's ex-boyfriend, who followed them to Seattle. While searching for Abby's friend, Nora Harris (Chelsea Tavares), Ellie encounters the Seraphites, a cult locked in a battle with the WLF over control of Seattle. Ellie tracks down Nora and tortures her for information on Abby's location, which traumatizes Ellie. The following day, she kills two more members of Abby's group, the pregnant Mel (Ashly Burch) and her boyfriend Owen Moore (Patrick Fugit). A flashback reveals that, years earlier, Ellie traveled to the Firefly hospital in Salt Lake City and learned the truth. Devastated, she cut ties with Joel. In the present, Ellie's group is ambushed by Abby, who kills Jesse and holds Tommy hostage.
Three days earlier, Abby learns that Owen, her ex-boyfriend, has gone missing while investigating Seraphite activity. Abby searches for Owen and is captured by the Seraphites. She is rescued by Yara (Victoria Grace) and Lev (Ian Alexander), Seraphite siblings who have been branded apostates after Lev defied Seraphite traditions. Though Yara suffers a broken arm, Abby leaves them to find Owen who, disillusioned with the war, plans to sail to Santa Barbara, California, where the Fireflies may be regrouping. Abby returns to rescue Yara and Lev, and travels across Seattle with Lev to retrieve medical supplies from the WLF hospital so Mel can amputate Yara's arm. After the surgery, Lev runs away to convince his devout mother to leave the Seraphite cult, forcing Abby and Yara to pursue him. They find him in the Seraphite settlement, where Lev has accidentally killed his mother in self-defense. The trio flee as the WLF begins an assault on the Seraphites. Abby betrays the WLF to save Lev, and Yara sacrifices herself to allow Abby and Lev to escape. The pair return to find Owen and Mel dead and a map left by Ellie leading to her hideout. Abby shoots Tommy, impairing him, and brawls with Ellie and Dina, overpowering them. At Lev's insistence, Abby spares them and tells them to leave Seattle.
A year later, Ellie and Dina are living on a farm, raising Dina and Jesse's son, though Ellie suffers from post-traumatic stress. When Tommy arrives with information on Abby's whereabouts, Ellie leaves to find her, despite Dina's pleas to stay. Abby and Lev arrive in Santa Barbara searching for the Fireflies, who they find are regrouping at Catalina Island, California, but are captured, tortured, and left to die by the slave-keeping Rattlers. Ellie arrives at Santa Barbara and rescues the pair. Threatening to kill Lev, Ellie forces Abby to fight her, during which Abby bites off two of Ellie's fingers. Ellie overpowers her but has a change of heart and lets her live. Abby and Lev sail to the Fireflies. Ellie returns to the farmhouse and finds it empty. She tries to play Joel's guitar with her damaged hand, recalls her last conversation with Joel in which she expressed her willingness to try and forgive him, and leaves.