Hershel tells Rick and his group that they have to leave his farm. Rick and Glenn go looking for Hershel. They find him in a local tavern. He is drinking large amounts of alcohol. After trying to get Hershel to go back to the farm, two other men enter the bar. They are with another group of survivors. This meeting does not go well and both men are killed in a gunfight. Other members of the group the dead men were with come looking for them. They find Rick, Hershel, and Glenn at the bar and begin shooting at them. The noise of the guns attracts a large group of walkers. While trying to get away from the walkers, the other group leaves one of their group, Randal, behind. Rick does not want to leave Randal to be killed by walkers. He cover his eyes and take him to the farm. Once they get him to the farm, they think that he could lead the rest of his group to the farm. Rick wants to drive Randall far away and set him free. While He and Shane are doing this, they are attacked by walkers when Rick and Shane get into a fight. Before the walkers attacked, Randall tells Rick and Shane that he knew Maggie. He knows where the farm is at. Rick thinks the location of the farm should be a secret to keep them safe. Since Randal knows where it is, they take him back to the farm until they know what to do with him. Rick and Shane talk about the fact that they will probably have to kill Randal. Back at the farm, Hershel's daughter Beth tries to kill herself. Seeing so many people in her family die, she does not want to live in this world anymore. The group talks about what to do with Randall. Only Dale thinks they should not kill him. While they are talking about Randal, Carl takes a gun from Daryl's motorcycle and goes into the woods. He sees a walker with its legs trapped in mud. Rather than shooting it, he starts throwing rocks at it. After a while, the walker gets free of the mud but Carl runs away. Later that night, the Rick and Shane go to kill Randal. As they are doing this, Carl enters the barn and tells Rick to shoot him. This causes Rick to stop and try to find a different way to deal with the problem. Soon after this, Dale is badly injured by a walker and will die soon. It is the same walker that Carl ran from earlier. Dale is then shot in the head by Daryl. This ends his suffering and stops him from coming back as a walker. Shane goes to the building where they are keeping Randal. He sets him free and takes him into the woods. Shane tells Randal he want to leave Rick's group and join Randal's group. Instead of this, Shane leads Randal from the farm and kills him by breaking his neck. The group sees that Randal is gone and starts to look for him. Shane goes back to the camp and tells them that Randal had gotten free, attacked him and taken his gun. Daryl, Glenn, Rick and Shane go looking for him. They separate into two groups. Daryl and Glenn are one group, Rick and Shane are the other. Daryl and Glenn find Randall. He has become a walker. They look at his body and see that he was never bitten. They understand that the dead can come back without being bitten. Shane uses the search for Randall to try to kill Rick. His plan does not work and Rick kills Shane. Just minutes later, Shane turns into a walker and stands up. Carl shoots him.
A very large number of walkers in the woods hear the noise caused by Carl's gun. They all start to walk in that direction. Rick and Carl run to the barn. Rick tells Carl to set the barn on fire after the walkers come inside. Rick and Carl leave the barn from an upper level while the walkers burn. With walkers all over the farm, a large battle takes place. Jimmy and Patricia are killed and Andrea is left behind. The rest drive away from the farm. Andrea runs into the woods. She is chased by many walkers. She kills many of them and is later rescued by a hooded woman. This woman, Michonne, is carrying a sword to kill walkers. She also has two walkers with her. These two walkers have had both of their arms and their lower jaws cut off. Michonne leads the armless walkers around with chains around their necks. The survivors all meet back on the highway where they lost Sophia. They drive off but must soon make camp when Rick's vehicle has no more fuel. Rick tells them that "this isn't a democracy any more" after he tells them what Dr. Jenner told him. Jenner told him that all of the survivors are infected. A large prison is shown in the be background as the episode ends.
The group have been on the road for months and Lori is far into her pregnancy. Rick finds a prison which was seen in the final scene in season 2. They decide to go to the prison and stay there. They kill the walkers outside and then go inside to kill some more. Hershel gets bitten in the leg and Rick has to cut it off. The group meet prisoners who had been in the prison's cafeteria for months. The prisoners had no idea what had been going on in the world since the outbreak started and Rick tells them about it. Some of the prisoners try to kill members of the group and so Rick kills Tomas and leaves Andrew to die while Oscar and Axel are put in another block away from the group. Andrew is still alive and rings an alarm which brings walkers to the prison. A huge battle happens. T-Dog is killed by walkers trying to protect Carol. Lori is about to give birth to her baby as this is happening. Maggie cuts her open to take the baby out but Lori dies. Carl is then forced to shoot his mother in the head. Rick finds Andrew and is nearly killed when Oscar shoots Andrew, killing him and saving Rick. After the attack, Maggie and Carl bring the baby to Rick. Rick finds out Lori died and starts crying.
After Lori has died, Rick starts to see visions of her. At the same time, Andrea and Michonne are found by Merle, who is Daryl's brother. Merle takes them to a town called Woodbury. The leader of Woodbury is a man who everyone calls The Governor. Michonne doesn't trust Woodbury and goes to the prison where Rick is. At the prison, Michonne meets Rick and his group. Glenn and Maggie are captured by Woodbury, so Michonne takes Rick's group to Woodbury to save them. In the battle, people on both sides die, but the prison group finds a way to escape. The Governor says to Woodbury that Rick and his group are terrorists.
Daryl reunites with his brother Merle after the battle and chooses to leave Rick's group with Merle. He changes his mind later and goes back to the prison group. Rick goes to his hometown to get weapons, and thinks about his morals when he sees Morgan again. Andrea convinces The Governor to speak to Rick and make an agreement for peace; secretly, The Governor plans an attack, and Merle risks his life to stop the attack. Andrea runs away from Woodbury but is caught by The Governor. He locks her in a room with a walker and attacks the prison. They are stopped by Rick's group, and The Governor kills his own people for not fighting. The Governor escapes, and Rick's group returns to Woodbury to bring in the survivors but are too late to save Andrea.
Several months later, the prison community has gotten bigger. Many people in the prison get sick with the flu at once. The flu kills many people who come back as walkers. Rick sends Carol away for murdering two sick residents. Walkers attack the prison fence and break it but are stopped afterwards. The Governor meets the Chambler family, and they join another group of survivors led by Martinez, who was in Woodbury before. The Governor kills Martinez and takes lead the group to attack the prison. Rick offers to share the prison, but The Governor calls Rick a liar and kills Hershel. The Governor fights Rick and is killed by Michonne, but the prison is taken over by walkers and Rick's group is divided.