Lori confronts Rick about her sexual encounter with Shane and the fact that her baby might be his, but before she can fully admit her mistake, Rick tells her that he knows, and that he just can't hear her say it. Glenn and Maggie are married by Hershel in a small ceremony in the prison's cafeteria. Life appears to go on as "normal" in the prison, with the survivors beginning to harvest their garden and even having basketball games.
Tyreese, Andrea, Glenn, Maggie, Michonne, and Axel go out in the RV to search for the national guard station used by the Woodbury survivors to stock up on weapons and supplies for the incoming onslaught from Woodbury. The group finds the base and takes several guns and canisters of gas, as well as a large army truck to gather even more supplies in. To prevent the people of Woodbury from taking more supplies, they blow up the depot. They then stop at an abandoned Wal-Mart for additional supplies, where they are confronted by Bruce Allan Cooper, Sam and a few other armed thugs from Woodbury. Glenn approaches the Woodbury men and attempts to negotiate but Bruce recognizes Glenn from his time in Woodbury and shoots Glenn in the waist. A gunfight breaks out, and the Woodbury men are defeated. Maggie rushes to Glenn, thinking he is dead, but his prison riot armor saved him. Glenn's ribs are badly damaged and the group quickly drives away from the site.
Back at the prison, Lori goes into labor. Billy Greene is sent to keep the generator on. He brings Dale with him, and they realize there is hardly any gas left to power the generator. They leave the prison gates to siphon gas from the cars in the parking lot, and Dale is bitten in the leg by a zombie. Glenn's party arrives at the same time and brings Dale and Billy inside. Lori delivers a baby girl with the help of Alice. Shortly after the birth, Dale's injured leg is hastily amputated by Rick. Lori then decides on the name Judith for her newborn daughter.
Dale, despite being bitten, seems to show no signs of turning. Following Dale's injuries, Andrea is spending more time with Tyreese. Dale suspects something, but Rick is convinced he is simply overreacting. Outside, the others capture a zombie and hold it hostage for study at Alice's request. Carol, meanwhile, is losing her grip on her sanity. After having sex with Billy, she goes outside and allows the captured zombie to bite her on the neck. The zombie is killed and Carol asks everyone to "let her die." Carol soon reanimates and is put down by Andrea. Dale learns to walk with a peg leg that Tyreese and Andrea made for him. Glenn and Maggie decide to try and have a baby. Just as life is settling down once again, Rick and Hershel look outside and see several cars and army trucks roll up. The Governor exits a functioning tank and orders his soldiers to 'kill them all'.
This arc begins with an extended flashback to explain what the Woodbury survivors have been doing. Michonne has mutilated The Governor horribly. His bodyguards, Bruce Allan Cooper and Gabriel Harris find him after breaking his door. Michonne is able to escape, and Bruce thinks she's dead when she leaves Woodbury. Bruce gets Bob, the town drunk and a former army medic. After a little fight with Bruce, he's ready to patch The Governor up.
A week later, The Governor wakes up. Gabe is with him, and tells the news. The Governor is surprised hearing Bob patched him up. Gabe informs him that Caesar Martinez left with Rick and the others. The Governor knows that, saying it was all his plan to discover the location of The Prison, and expects Martinez to return soon. After recovering in his apartment, Bruce comes to tell him they have found Martinez, zombified.
The Governor speaks to the gathered Woodbury people and tells them that the prison survivors are a group of savages who must be destroyed. While they begin searching for the prison, Bruce is fatally shot by the survivors after they raid the guard station. The Governor shoots his friend in the head. Gabe finally locates the prison while the survivors are having shooting practice, though the governor plans to wait longer and pull them into a false sense of security. The Governor finally prepares his large army and they leave for the prison in numerous cars, trucks, and also bringing a functioning tank. As the shooting begins, Rick and the others dive for cover while Andrea climbs to the top of the guard tower. The Governor ceases fire to offer surrender to the prison survivors, though he quickly gives up and orders the army to resume firing. Rick quickly runs inside and tells Lori to take Judith and head underground and hide. Andrea begins picking off men from the army. She is however, non-fatally shot in her attempt to shoot; killing many before passing out. The Governor tries to intimidate the group by using his tank to clear away the piled zombies at the gate. Despite superior numbers, the Woodbury army is poorly trained and are forced to fall back as Andrea kills too many of them. Rick's group begins to debate whether they should remain inside the prison or go on the offensive. Before they can decide, Rick emerges from the prison with a bullet wound in his abdomen and collapses. He, Andrea, and a wounded Axel are taken to the prison hospital by Alice.
Dale, Andrea, Billy, Ben, Sophia, Glenn, and Maggie Greene flee the prison in the RV in order to avoid the confrontation they expect from The Governor. Rick gets a blood transfusion from Patricia and starts to recover. Tyreese and Michonne decide to tail The Governor and the townspeople in the hopes that if they kill a few more, it will discourage their attack. Tyreese is captured after killing a couple townspeople and is told that Michonne is dead. The survivors still inside begin to prepare, though many of them believe they will not survive another attack. The Governor returns to the prison with Tyreese as his prisoner. He tells them he has Michonne as well and they must let him in or Tyreese dies, with Tyreese selflessly shouting at the survivors not to let them in. The survivors refuse to let him in and The Governor decapitates Tyreese using Michonne's katana. They leave Tyreese's body in front of the prison gates for the zombies as they flee. The Governor tells the Woodbury people a false story about how Rick and his people killed Tyreese, but Michonne then shows up right behind him with a gun to his head. Gabriel Harris opens fire at Michonne, but she fires back, clips The Governor, kills one of his men and escapes. The Governor and his army return to the prison and launch another attack. Axel is killed, but the prison survivors are able to successfully defend themselves. The Woodbury army is further destroyed and demoralized by Billy hurling a grenade into their midst, killing several of them. Gabe tells The Governor that Woodbury's army must regroup, but The Governor refuses. Gabe is shot and killed by a returning Andrea in the RV. One of The Governor's henchmen drives a truck into the RV, injuring Andrea. As his army seeks to retreat, The Governor orders the IFV to drive over the fences. Rick and his group rush to escape while The Governor and his army invade the prison. Rick rushes into the cell-block, looking for Lori and Judith and eventually finds them with Alice pointing a gun at them. Alice explains that it was a ruse in case The Governor found them.
Rick, along with his family and Alice, attempt to escape to the truck. Meanwhile, Patricia and Billy Greene are shot and killed by the overwhelming number of invading soldiers. Billy's death demoralizes Hershel to give up. Rick gives up their position by yelling for Hershel. The Grimes family attempt to get to the truck under heavy fire while Alice covers them. Alice is quickly gunned down and executed by The Governor. Shortly after, Lori and Judith are both killed by Lilly who shoots Lori in the back with a scatter gun. Lori falls to the ground, crushing Judith, as Rick watches in horror while attempting to escape with Carl. The Governor orders his men to stop firing at them, as he is certain they will be overwhelmed by the zombies out in the open, and then executes Hershel. Lilly realizes that Lori was carrying a baby and calls The Governor a monster. She hits him with her rifle and puts the barrel in his mouth. A horde of zombies, however, break through the hole in the fence and attack the Woodbury army. The Governor gets up, shoots a zombie and urges the group to move into the prison, yelling that they can still rebuild the ruined prison later. As the remnants of the army are overwhelmed, Lilly gets to her feet and shoots The Governor in the head and pushes his corpse into a mass of zombies, buying the Woodbury army time to flee. She then leads the remnants of the army into the prison. They are eventually heard running out of ammo as the prison is overwhelmed by masses upon masses of undead. Rick and Carl narrowly escape the prison and embrace each other after experiencing such devastating losses. The prison in ruins behind them as zombies approach.