In the years following the outbreak, Tommy and Joel made their way to the Boston Quarantine Zone but the actions committed by the brothers in order to survive caused Tommy to suffer "nightmares from those years". Sickened by Joel's growing inhumane activities and the military's tyranny, he decided to join the Fireflies, after being convinced by Marlene. He was filled with hope that the world could get better, which led to an argument between him and Joel which ended with them parting ways, Tommy's last words to Joel being, "I don't ever want to see your goddamned face again."

He spent a long time with the Fireflies, even visiting the group's main research lab in the University of Eastern Colorado. Tommy eventually left the Fireflies after becoming disillusioned with their cause. Before he left, he informed Marlene she could rely on his brother if she was ever in need of assistance. He left a strong impression on her, causing her to remark years later "he was a good man". Tommy eventually reached Jackson County, where he helped to make it into a safe haven. He married a woman named Maria and they become the leaders of the settlement while trying to get the generator fixed.

The hydroelectric plant is under constant attack by bandits. For a few months Tommy traveled back to the brothers' hometown in Texas; most of their things were long gone, though he retrieved a slightly faded photo of Joel and Sarah at a soccer match. During the Fall of 2033, Joel and Ellie stumble upon a seemingly abandoned power plant in Jackson County, Wyoming while trying to find Tommy.

To their surprise, Tommy, Maria, and many of their men were trying to get the power plant up and running again to power their settlement electrically. Tommy greets his brother with open arms and welcomes him into the plant, introducing him to Maria. After showing Joel around and getting the power back on, Joel gives Tommy the information regarding Ellie's immunity to the CBI, expecting Tommy to heed his order to take over the delivery of Ellie. Due to leaving the Fireflies and their cause behind him and the danger of the journey, Tommy refuses to deliver Ellie to the group, realizing that Joel hasn't changed since he last saw him.

An argument ensues, in which Joel indirectly insults Tommy's community and the memories of their dark past resurface, leading to an enraged Joel shoving his brother, but they are interrupted by a bandit attack. Tommy, with help from Joel and some of his men, fends off the attackers. Tommy reconsiders his decision to take Ellie to the Fireflies' lab after seeing her interactions with Joel. Maria is understandably upset when Tommy tells her this, knowing that she may end up being a widow if Tommy made even one mistake.

Before he can leave with Ellie, she steals a horse and runs away. Joel and Tommy give chase, tracking her on horseback through the woods and arriving at a narrow pass with a couple of cabins before they are ambushed by the Bandits there. Tommy provides covering fire while Joel pushes up the pass towards the cabins and the duo wearily kill their attackers. Following the skirmish, the two continue to follow Ellie's trail and find her at an abandoned ranch. Realizing that the two likely have some talking to do, Tommy keeps watch downstairs.

After a while, he notices more bandits have tracked them to the ranch, so he runs upstairs to alert Joel and Ellie of the incoming danger. They fight their way out of the house, regrouping outside. After offering Ellie help onto her horse, Tommy and the others ride on horseback back to the dam, where Tommy shows them how he has turned Jackson County into a small fortified town, now with electricity, enabling the children to watch television.

Joel tells Tommy he will take Ellie and Tommy can go back to Maria proving himself to have changed. Tommy tells them that the Fireflies' lab is in the University of Eastern Colorado. As Joel is about to leave with Ellie, he offers them both sanctuary in his town, saying there is always a place for Joel. Joel doesn't answer, giving the impression of acceptance, and instead bids Tommy farewell before riding off. Months later, after Joel rescues Ellie from the Fireflies in Salt Lake City, they return to Jackson County, intending to live in Tommy's settlement.

When Joel does return, Tommy accepts them as he promised, giving them a room each but has them working on fortifying the defenses while they live there. He introduces Joel to a woman named Esther, Joel believing that he intends to have them "hitched".