- "Seed"
Hershel and the rest of the group discover a prison Rick believed could be their new home. Before settling into the prison, Hershel talks to Rick about Lori and the possibility that she may have lost the baby due to stress and over exerting herself. Hershel and the others went into the prison's fence and Rick assigned Hershel to shoot the walkers from one of the towers together with Carl. That night, Hershel suggested that they should plant some seeds so they can grow crops. Also, Hershel asked Beth to sing one of Paddy Riley's song at the campfire, but Maggie declined by saying "Daddy, not that one please." Hershel then changed his request and told Beth to sing "The Parting Glass." Beth then proceeds to sing, and Maggie eventually sings along with her sister. The day after Rick, Glenn, Daryl, T-Dog, and Maggie cleared out cell block C, Carol called for Hershel to come over as Lori wanted to talk to him about the baby. Lori expresses to Hershel her fears and assumptions that her son can't stand her and that Rick hates her for putting him in difficult situations. That day, Rick, Daryl, T-Dog, Maggie, Glenn, and Hershel attempt to clean out another section of the prison. The group soon runs into small herds of walkers and is forced to retreat. During this, Glenn and Maggie become split up from the group by walkers and lock themselves in a closet.
The group, noticing the disappearance of the two, plan to go back and search for them. While they are searching, Hershel is seen stepping over what appears to be a dead inmate. The group circles back, safe from the walkers and Hershel is again seen stepping over the inmate, which shockingly awakens. The formerly dormant walker grabs Hershel by the leg and bites into his calf. Rick shoots the walker in the head and the group quickly responds to the tragedy that has taken place. They are last seen inside a vacant cafeteria where Rick examines the bite. Rick, quickly thinking, removes his own belt and ties it above the bite before taking a hatchet and messily amputating Hershel's lower leg to save him. During the amputation, Hershel loses consciousness. Stuck inside the cafeteria, the group looks up and sees a group of living inmates staring back at them.
- "Sick"
Hershel is rushed into one of the cells in C Block, and the team attempts to stop the bleeding. Carol eventually slows it down with help from Carl who retrieved medical supplies from the infirmary. At one point during the episode, Hershel appears to stop breathing. Lori checks his pulse multiple times, and eventually gives him mouth-to-mouth CPR. He soon darts up and grabs Lori in much the same way the dormant walker had grabbed him, but she is pulled away from Hershel. He appears to be alive, as his eyes are still their normal color, and he soon falls back asleep. As a precaution should Hershel turn, he is handcuffed to the bed frame. Soon, when Rick returns from helping the other prisoners clear another cell block, and enters the cell Hershel is in, Hershel wakes up. He raises his hand, and holds Rick's hand, but doesn't say a word. He soon falls back asleep.
- "Killer Within"
Hershel is shown in this episode to have recovered well from his amputation and is beginning to walk with crutches. When Walkers start to pour into the prison after Andrew took his revenge, Hershel and Beth hide behind a gate and remain there throughout the episode. At the end of the episode, Hershel is present when Maggie emerges from the prison carrying Lori's newborn child in her arms and witnesses Rick's sad, distraughtfit. Hershel appears to be saddened by Lori's loss as well.
- "Say the Word"
Hershel appears in this episode standing on his crutches, talking to Glenn as he mourns the deaths of Lori, and T-Dog. While Hershel believes that the two remaining prisoners, Axel and Oscar, are good people, Glenn believes that all of the prisoners should have been killed at first sight.
- "Hounded"
Hershel is seen first in the episode, eating with the others in the cafeteria of the prison. He later visits Rick, who is still in the prison's boiler room waiting for the phone. Rick tells him about another group of survivors, and how he is trying to join up with their group for safety, but tells Hershel not to say a word to the others about it. Hershel offers to sit with Rick, but Rick says no. Hershel is seen holding Judith when Rick returns to the group a second time. He passes Judith to Rick, who has finally come to embrace his newborn daughter. Afterwards, he, Rick, Judith, Carl, and Beth walk triumphantly out to the prison-yard as the group realizes that things seem to be looking up.
- "When the Dead Come Knocking"
Hershel is seen behind Rick as he opens the gate to retrieve Michonne's unconscious body. He also asks Rick if Michonne has any bites on her, to which he replies that it is only a gunshot wound. He is seen with the other survivors as they interrogate Michonne. He is also seen stitching up Michonne's gunshot wound (inflicted by Merle). Afterwards, despite the gentle treatment, she replies with a stern "thank you."
- "Made to Suffer"
Hershel appears mostly by Beth's side during this episode. Hershel puts Judith to sleep in her crib and talked to Beth and Carl, sitting on the stairs. When Carl hears a noise emanating from elsewhere in the prison, Hershel attempts to stop him from investigating the noise but ultimately decides to let him go. He is later seen when he sees the new group arriving in another cell. Sasha Williams glares at him and yells at them to unlock the door when Carl locked it. Tyreese, Sasha's brother and the leader of the group, calms her down and gives Hershel and the group his assurances that they're not looking for trouble.
- "The Suicide King"
Hershel is seen in the common room, doctoring Allen's leg. Hershel bonded with Tyreese and the two share some of their stories since the outbreak began. Hershel told Tyreese that he shouldn't get too comfortable here, as he can't make the decision whether Tyreese's group can stay here or not. When Rick, Glenn, Maggie, and Michonne return to the prison, Hershel and Beth hug Maggie and he tells Beth to take her sister inside to get some medication. Back in the cell, he examines Glenn's injuries, surprised that Glenn sustained no broken bones. He informs Glenn that he is like a son to him, before leaving to talk to Maggie. Hershel told Maggie if she has anything to talk about, she can talk to him. He also mentions how he noticed her strange behavior around Glenn. He told her that he is proud of her and that she got her mother's spirit and stubbornness. She laid down in his arms and the two bonded with each other. Later that evening, Hershel wanted Rick to let Tyreese's group join them. When Rick says no while deciding the fate of Tyreese's group, Hershel argues against the decision due to their shortage in manpower following Oscar's death and Daryl's abandonment. Shortly after, Rick screams around the room, and Hershel stared at Rick, confused about his act of sudden tantrum.
- "Home"
After Rick's outburst towards the hallucination of Lori and indirectly towards Tyreese, Hershel is seen with the group inside of The Prison. He listens to Glenn's proposal on how to defend themselves from The Governor, but recommends that the group leave the prison rather than risk retaliation from Woodbury. He later comments that Glenn's decision to take over the leadership from Rick may be unwise at this time since Maggie is still recovering from her and Glenn's detention and torture in Woodbury, also advising Glenn to comfort Maggie. Later, when Glenn is outside and about to leave the Prison to scout, Hershel advises him to stay and take stock. Glenn ignores his council and leaves. Distraught, Hershel notices Rick wandering outside the Prison. There, he notices Rick outside of the fence, deciding to counsel him about his mental status. Rick confesses to Hershel about his visions of Lori and Shane, and Hershel urges him to come back inside of The Prison, where it is safe, but before Rick refuses. Just then, The Governor attacks them. Hershel ends up pinned down within the prison fence where the "walker bomb" is deployed. Hershel is rescued by Michonne and Glenn before he can be harmed.
- "I Ain't a Judas"
Hershel is seen with the rest of the group discussing the Woodbury situation. When Rick attempts to wander off, Hershel yells at him to get back here and do something, but Rick ignores him and wanders outside. Hershel visits Merle in his cell, where they bond over their amputations and a Bible verse. Merle tells Hershel of The Governor's planned pecking order during a second attack, with Merle being the first death and Rick being the last because The Governor wants Rick to watch his family and friends die around him. Andrea returns to the Prison, and appears shocked to see that Hershel has lost his leg. He then informs her of Lori's fate and the birth of her baby girl,and asks why she's so sure that The Governor is willing to negotiate. Later that night, while Beth is singing by the candlelight, Hershel voices his concerns about Andrea's inner conflict and The Governor's numbers. Rick agrees and says that they need to match those numbers,then decides to go for a supply run in the morning with Michonne and Carl to try and find some bullets and new weapons. Rick then tells Daryl and Hershel that they will be in charge while he's gone.
- "Arrow on the Doorpost"
Hershel goes along with Rick and Daryl to the meeting with The Governor. Later, he is seen talking to Milton Mamet about his amputation, and even jokes about his question regarding the leg. The two seem to form a bond of sorts because of this. When the meeting is over, he leaves with Rick and Daryl. Back at the prison when the meeting is over, Hershel privately mentions the group's sentiments about going to war with Woodbury. He and Carol think the group should leave the Prison behind and take their chances on the road to avoid any more hostility from Woodbury and The Governor, but they would go along with whatever Rick felt was best. It's then that Rick reveals the truth: the Governor asked for Michonne. Hershel stands up for Michonne, saying she earned her place. However, when asked if he would risk Maggie and Beth's lives for her, Hershel cannot counter.
- "This Sorrowful Life"
Hershel is still against the idea of Rick handing over Michonne to The Governor, and agrees with Daryl when he says that the decision is not like them. Later on, Hershel and his daughters pray with a bible and he said he would do anything to keep Maggie and Beth away from harm. While in his cell, Glenn visits him and says that he now understands why Hershel gave him the pocket watch and tells Hershel that he wants to marry Maggie. Hershel gives Glenn his blessing. Hershel is later seen on the outside of the Prison, along with the other remaining members of the group as Rick denounces having sole leadership.
- "Welcome to the Tombs"
Hershel is first seen packing important medical supplies in bags. He then hides out in the woods with Carl as the Woodbury army ambushes the Prison and retreat when they are ambushed themselves. Jody, one of the Woodbury soldiers, runs off into the woods where he comes across Hershel and Carl. Despite surrendering his gun, Carl shoots him anyways. Hershel tells Rick about what really happened with Jody, as Carl had lied to Rick. Hershel tells Rick that Carl gunned Jody down and Jody had no intentions on killing either of them.
Later, at the end of the episode, Hershel cheerfully guides the remaining Woodbury survivors to their new home in the Prison, most of whom are children or elderly.
