The episode opens with someone from inside the prison shining a flashlight, and then dangling a rat, in front of the walkers at the fences to incite them. Inside, Tyreese and Karen are making out, but he can't stop thinking about Zach, so they stop and have a bit of a philosophical conversation. He starts singing "Under My Skin" to her, and they're having fun up until she says they should try to get some rest. He offers for her to crash with him, but they part ways instead. She leaves his room and walks down the hallway, stopping to look at pictures drawn by the kids in the prison's classes and to splash some water on her face. In the shower room, she hears a noise and goes to check it out--which of course is when she fails to find Patrick, who died in the final seconds of the previous episode and is just now reanimating. She heads back to her cell and the walker follows her--but before he can walk into her room (they're not locked cells; everyone seems to have sheets for "doors"--someone down the hall a bit coughs and he follows the sound; that person doesn't even wake up before the walker chomps out his throat. Apparently nobody notices the sounds of the devouring because when we cut back to the prison after the credits, he's still sitting on the floor in that guy's room, having mostly eviscerated him and eating his entrails. He hears another cough, goes to investigate, and the guy he was just eating reanimates, too. Outside, there's a horde of walkers at the fences. Glenn and Maggie are still spending some time in the guard towers, apparently, and Glenn takes out the camera he got in the previous episode and takes a picture of Maggie sleeping. This wakes her up, and he promises her to bring breakfast after perimeter check. She tells him to throw away his Polaroid, and he says no and goes off to take guard duty.
Rick and Carl are headed toward the garden while Michonne gets her horse and moves out to look for supplies and, presumably, The Governor. Carl notices that the walkers at the gate are pretty plentiful and suggests that they should help out, but Rick says that he has plans for farming, and that Carl has to help him. While they're feeding the pigs, Carl asks when he can have his gun back. Rick ignores the question. There's a bang in the distance, and Michonne turns back while Carl heads to the gate to let her in. Some walkers follow her in and she has to push them back and then take them out, something she does with the help of Carl and Maggie but Michonne is injured in the process. They notice that all of the walkers are leaving them to head for the gates. Inside the prison, there's a bit of a panic brewing as a handful of walkers are devouring others and the people in that cell block are trying to evacuate. Rick, Carol and Tyreese are among those who come in to help, with Carol stopping to amputate the arm of a man who was bitten. She realizes that he was also bitten on the neck, though, while she's inspecting him. Tyreese, in particular, makes a beeline for Karen to make sure she's okay.
Glenn, Rick and Daryl finally clear out the final walker--Patrick, who attacks Glenn and is killed by Daryl's crossbow. They begin clearing the cells, with Daryl having to destroy the brains of some people who had been killed but not yet reanimated. Rick pulls out his knife and heads into a cell that apparently needs similar work done, and then emerges holding it clumsily. In the cell with Carol, the man she's working on has figured out that he's about to turn. He asks Carol to take care of his kids after he's gone, "like they're yours." She agrees to do so, and then asks if she can bring them in to say goodbye to him. In one cell, a walker comes up to the bars and approaches Rick, who stabs it in the head. Looking over the bodies, they realize that at least two of them--Patrick and another--had died by choking on their own blood and that nobody had been bitten. It's an aggressive flu strain, apparently; while Daryl is very surprised that he died so soon, Rick says he had a pig that died suddenly. They start strategizing what to do about the flu. In the dying man's cell, the girl who spoke up to Carl last episode comes in to watch her dad die. He tells her to take care of her sister. Carol tells them that she has to destroy him before he turns, but that they can wait outside if they want. The younger girl wants to leave but the older girl says she should be the one. Carol gives her a knife and she looks at him for a moment and then starts to hyperventilate. Carol puts a knife in their father's ear while the younger girl tries to calm her older sister.
Outside, Carl rushes into Rick's arms. He admits to having used a gun but Maggie and Michonne tell him it's okay. In the prison library, Hershel talks with Carol, Glenn and Sasha, who are trying to figure out how to manage the quarantine. Karen walks by with Tyreese outside the room and is coughing, so they stop her from going back to her cell and tell her she needs to be separated. She tells them about another survivor ("David from the Decatur group") who is coughing, too. Glenn goes to get David. Daryl says he's going to start burying bodies, and Hershel tells him that he needs to wear gloves and a mask when doing it. Daryl and Carol talk about their next step, especially keeping an eye on the girls Carol is now de facto mother to. She goes out to the wall to talk to them, but Lizzie (the older girl) won't listen to her. Carol tells her that you can't be weak--that you can't lose your nerve, because mistakes like she made in the cell are life and death. "If you want to live, you become strong," she said. Lizzie runs off babbling, and her little sister tells Carol, "She's messed up, she's not weak." Outside the gates, Daryl is burying the bodies when Rick comes to help with the digging. Daryl asks him to help figure out the situation. Rick said that he screwed up too many times when he was the leader, but whatever else the prison needs, he's there for. Magggie comes after them, screaming, because the outer fence is about to give. The three of them, plus Tyreese and Sasha, start taking out walkers on the other side of the fence but Rick is freezing up in between strikes, unconfident.
Back inside, Beth is wrapping Michonne's ankle while Judith plays on the floor. Michonne says she was stupid--that she fell on her ass and they should have just left her. Beth is uncharacteristically sage, but their conversation is broken up when Judith starts screaming and Beth takes her out of the cell. Outside, Maggie falls over while they're clearing out the gates. Sasha finds a bunch of dead rats and figures out that someone is feeding the walkers. They don't have long to deal with that, though, because the fence around them starts to give and they have to start moving back away from it. Rick tells Daryl to go get a truck--that he knows what to do. Inside, Carl is putting together burial crosses for the dead. Carol walks up and asks him whether he told Rick that he saw her teaching the kids in the library about knives. She says she has to keep teaching them survival skills, but that their parents don't know. She doesn't want to take the risk of the parents failing to understand. Carl tells her that's between her and the parents, but Carol says that it's between her and Carl, since if he tells Rick, Rick will notify the parents. Carl is hesitant to lie to his dad, but she says all she's asking is that he remain silent, not to lie. Back in her cell, Michonne is exercising and worrying that Judith's cries sound abnormal. When Judith spits up on Beth, she asks Michonne to hold the baby and Michonne is resistant, but then takes her. She looks at the baby, starts to cry and then holds her close. Outside, Rick and Daryl are driving a Jeep out behind the walkers on the dirt road, with a large box on a trailer. When they stop, Rick takes a pig out of the box, cuts its hindquarters and throws it to the walkers. When the walkers all huddle around it he drives on, then stops to repeat the process; each time, the walkers bunch up but stop and they're all being driven away from the prison so that Tyreese and Sasha can shore up the fence. Rick is visibly upset about what he has to do here, but given that the pigs had been identified as a risk for the flu, it does seem to solve two problems at once.
Back at the inner gate, Lizzie and her sister are looking at the walkers at the outer gate, and Carol comes up to them to try and console them and lend perspective. She cuts a flower for Lizzie, puts it in her hair and gives the girl the knife. Carl comes to the pen, where Rick is about to burn it down, and Rick tells him that the pair of them should stay away from Judith for a while. Carl agrees, saying they have to protect her. Rick seems proud of Carl in this, but it only lasts a moment before Carl drops the bomb about what Carol is doing--and that he thinks Rick should allow it to continue. Rick doesn't respond right away, dumping out gas on the remnants of the pen and thanking Carl for telling him, and then telling Carl that he won't say anything before setting the controlled burn. He pulls Carl aside and gives him his gun back, then puts his own gun and holster on as well. he tousles his son's hair and then pulls his own shirt off and throws it on top of the fire (it's covered in the pigs' blood). Back at the gate, walkers are starting to mass again. Tyreese brings Karen a bunch of flowers, only to find that she's got a trail of blood leading from her pillow, out of her room and down the hall. He follows it outside to where he finds a pair of charred bodies--one of which is apparently Karen's and the other is a male.