The Governor first appears in the third episode of season three, having kidnapped Andrea and Michonne from the woods after discovering them near a downed military helicopter. He murders the surviving soldier, Lt. Welles, after Welles tells him where the rest of his squad is. When The Governor arrives at the squad's encampment, he and his men shoot them all to death and take their supplies. While concealing all of this from Andrea, he and Andrea begin a relationship. Woodbury, under his rule, is a community that thinks of him as a kind and caring leader. However, Michonne accurately describes him as a "Jim Jones type", and his supply parties are, in truth, bandit raids. The Governor's name is Phillip Blake, and he has a zombified daughter named Penny, whom he keeps hidden, feeds body parts to, and grooms affectionately while playing a lullaby. Michonne uncovers clues that indicate he is mentally disturbed, including a notebook that begins as a sort of urban planning diary that devolves into list of names followed by pages of disturbing tally marks.

In the midseason finale of season three, during Rick's foray into Woodbury to rescue Glenn and Maggie, Michonne kills Penny, The Governor attacks Michonne, and in self-defense she stabs him in the hand and the eye with a glass shard. He then proceeds to rally Woodbury against the prison survivors, labeling them terrorists and raiders. Encouraged by Andrea, he eventually meets with Rick in a secluded area to offer him peace in exchange for Michonne (while actually planning to kill all of Rick's group and torture Michonne). Later on, his relationship with Andrea ends when she finds out about his dark, sadistic, duplicitous nature. Merle kidnaps Michonne two days later, but lets her go and instead lures walkers to The Governor's meeting place to ambush the Woodbury army. After Merle shoots eight of The Governor's men, The Governor shoots and kills Merle, leaving his body to reanimate as a walker, which is later killed by Daryl.

In the season three finale, The Governor leads his army into the prison to kill Rick's entire group, but Rick and the others have set a trap, expecting his arrival. Ambushed and outgunned by a very prepared Maggie and Glenn in riot gear, The Governor's army flees the prison in terror. The Governor stops the fast-fleeing convoy, and, in response to their protests against returning to the prison, he opens fire and slaughters them all, sparing only Caesar Martinez and Shumpert, his two best henchmen. A Woodbury resident, Karen, escapes his rampage by playing dead. As the season ends, The Governor, Martinez, and Shumpert's whereabouts are unknown.

In season four, Michonne has been actively hunting The Governor, but is failing in her endeavor and intends to continue her search into Macon. The Governor does not appear in this season until the fifth episode, during which he is very briefly shown hiding just outside of the prison. The following episode reveals that, just after massacring his own people, The Governor sets up camp with Martinez and Shumpert. However, they abandon him after he shows no reaction to a walker attempting to attack him, forcing Martinez to shoot it. The Governor drives back to Woodbury, which is overrun with walkers, and burns down the entire town. After several months alone, he finally collapses on the street. He looks up to see a young girl, about the same age as his dead daughter, in the window of a nearby apartment building; he pulls himself back to his feet and investigates. He finds the Chambler family residing inside, consisting of sisters Lilly and Tara, their father David, and Lilly's daughter Meghan (the young girl in the window). Lilly and Tara initially hold The Governor at gunpoint, but they later confiscate his pistol and allow him to stay in an apartment across the hallway.

After hearing about how The Governor has survived the last few months, they ask him his name. He tells them that it's Brian Heriot, a name he saw painted on the side of a barn while staggering aimlessly through the countryside. Lilly later comes to the apartment where he is staying and offers him some food; he accepts it, but after she leaves, he throws the food out of the window and continues eating a can of tuna he found. He goes to their apartment to return the plate and is invited inside. He runs some errands for the family, such as getting the backgammon set that one of David's old war friends had in his apartment on the floor above them, since playing backgammon is the only thing that makes Meghan happy. The Governor finds the backgammon set and a few rounds of ammo in the apartment. He kills the walker of David's friend and takes a revolver from it. He returns to the Chamblers' apartment, gives David the backgammon set, and leaves.

Lilly asks him to get some oxygen tanks for David, who has cancer and whose last tank is running out of oxygen. After several struggles with walkers at a nearby nursing home, The Governor is able to escape with two oxygen tanks. Lilly thanks him and cleans a minor head wound that he received. She lets Meghan stay and watch him while she goes back to their apartment; Meghan asks him how he got his eyepatch, and he says that he'll tell her the truth if she doesn't tell anyone. Later, he is teaching Meghan how to play chess when Lilly reveals that David has died. The Governor tells the surviving Chamblers to leave David's room, as he knows that David is about to reanimate, but Lilly wants another minute alone to say goodbye. David turns and nearly bites Tara, but The Governor is able to save them by bashing David's head in with one of the very oxygen tanks he grabbed from the nursing home. After he buries David, he burns his photo of his wife and daughter.

That night, he goes to the Chamblers to say goodbye, but Lilly insists that he stay. The Governor says they can't go with him, but Lilly reveals that she saw the photo of his family. She admits that they aren't his old family, but he has become a part of theirs. The group leaves the building in a delivery truck parked outside. After camping at a lake, their vehicle breaks down, forcing them to abandon it and continue on foot. The Governor and Lilly sleep together. Down the road, Tara injures her leg. The Governor goes ahead and, seeing a group of walkers, orders them to drop their bags and run. While the rest flee, Meghan freezes in place, and The Governor convinces her to run to him. He then picks her up and leads the others through the woods. As they reach a clearing, The Governor and Meghan fall into a pit and find several walkers inside. Meghan cowers in a corner as The Governor kills the walkers with his bare hands, ripping out their throats and punching their heads in. Gunfire can be heard in the background, but it stops soon after The Governor kills the walkers. He hugs Meghan and promises that he will keep her safe from anything that may harm her. He hears a surprised voice coming from outside the pit. He looks up and sees Martinez standing above him.

Martinez takes The Governor and the girls in and lets them join their camp. Among the camp are brothers Pete and Mitch, who have a working tank. When it becomes clear that Martinez may not be able to keep them safe and offers to share power with The Governor, The Governor kills him by throwing him into a pit of zombies. Pete takes command. Later, The Governor kills him as well and takes control of the group. He plans to rally them and use the tank in a second attack on the prison. He takes Hershel and Michonne hostage, and goes to the prison with his people and the tank. Meanwhile, back at the camp, Meghan is bitten by a walker from the river bank that was buried in the mud. Upon arriving at the prison, the Governor tells Rick that he is going to give their group a chance to leave without anyone getting killed. Rick tries to plead with The Governor, but the Governor is completely deaf to his pleas, as he holds Michonne's sword to Hershel's neck, eventually slicing it open; when Hershel, still barely alive, drags himself away in the ensuing chaos, The Governor brutally decapitates him as Hershel's daughters look on from the prison. The Governor then launches his attack on the prison, rolling the tank over the gates and firing at the prison. Lilly eventually arrives, approaches him with Meghan's corpse, which he takes and wordlessly shoots in the head. He goes into the fight himself and begins firing, only to be tackled by Rick. The two of them fight, and The Governor eventually pins Rick and brutally beats him before beginning to choke him. The Governor is then stabbed through the back by Michonne, who decides to leave him to bleed to death. Towards the end of the episode, a dying and barely-conscious Governor is approached and shot in the head by Lilly. In the opening of the next episode, his corpse is seen laying on the ground as Michonne escapes the prison grounds.