In the episode "Alone", a flashback set a week before the season premiere shows Glenn and Daryl on a run when they encounter lone survivor Bob Stookey, who reveals he is the last survivor of two previous groups who were all killed. Daryl asks how many walkers and people he has killed, and Bob states that he has killed a few dozen walkers and one woman, on her request. After deeming him trustworthy enough, Glenn and Daryl give Bob a ride back to the prison.
In the season premiere "30 Days Without an Accident", Daryl has become popular among the growing population at the prison for his proficiency at hunting. Daryl goes on a supply run with Sasha, Tyreese, Glenn, Michonne, Zach (Beth's new boyfriend), and Bob. Zach is bitten by a walker and killed, and when Daryl tells Beth the bad news she does not seem upset, and she claims that she has lost too many people to get upset anymore; Daryl confesses to being sick of seeing people die, and Beth hugs him. In the episode "Infected", Daryl helps clear out the cellblock when walkers attack, and the group finds out that a deadly infection is spreading among the population. Daryl and the rest of the prison's council agrees to start quarantining the sick, including Karen and another prisoner named David. In the episode "Isolation", when Tyreese goes looking for Karen and finds the burned bodies of Karen and David, he shows Rick, Daryl, and Carol. Daryl, Michonne, Bob, and Tyreese head to a veterinary college in search of antibiotics. They hear a message On the car radio, offering sanctuary at a place called Terminus, before the car is swarmed by walkers and they are forced to flee on foot. In the episode "Indifference", Bob confides his alcoholism to Daryl. They retrieve the medicine from the college, but Bob is nearly pulled into a group of walkers when they grab his bag. When Daryl finds a bottle of alcohol in the bag, he threatens Bob not to have a drink before treating the sick with the antidote. In the episode "Internment", they return to the prison with the medicine, and Bob administers the antibiotics. In the mid-season finale "Too Far Gone", Rick tells Daryl that he banished Carol from the prison because she killed Karen and David. They go to tell Tyreese about this, but they are interrupted by the sound of an explosion before they can tell him. During the Governor's second assault on the prison, Daryl helps fend off the attackers, even blowing up a tank. Daryl escapes the prison with Beth.
In the episode "Inmates", after the group is split, Daryl and Beth are on the run together. Daryl acts despondent and says very little as they sit by a campfire. In the episode "Still", Beth and Daryl then find a moonshine shed much like the place Daryl grew up in, and stay for a bit. They get drunk and play a game of "Never Have I Ever", which leads to Daryl yelling at Beth after he gets offended by a question asked by Beth. He then drags her outside to shoot at a walker and gets into an argument about whether or not anyone else survived the prison attack. After they talk a bit and before they left they burn the house down with the moonshine and some money, flipping it off as it burns. In the episode "Alone", Daryl and Beth come across a funeral home, where they start to form a bond. When Beth asks Daryl what made him change his mind about whether there are still good people around, he simply stares at her, implying that she was the reason he changed his mind. Their moment is interrupted when Daryl hears what he thought was a dog at the door and opens to reveal a walker herd. Daryl fights off the herd, but Beth gets kidnapped in the chaos. Daryl runs after the car until morning, but stops after he comes to a fork in the road. He is then approached by a group of bandits led by Joe, and decides to join them when given the choice between joining their group or being killed. In the episode "Us", Daryl travels with Joe's group, learning its rules about who "claims" what and that they are tracking a man who recently killed one of their own. He also comes to aggressive odds with a member of the group when they indirectly mention Beth by saying, "I bet it's a bitch that's got you messed up", which almost prompts Daryl to kill the other member. In the season finale "A", Joe's group eventually catches up to the man they are tracking, who turns out to be none other than Rick Grimes himself, along with Michonne and Carl and captures them. Daryl pleads with Joe to spare them as they are "good people". Joe calls him a liar and has two men try to beat him to death. However, when Joe informs Rick that the group is going to rape Michonne and Carl before killing him, Rick surprises everyone by biting out a chunk of Joe's neck, killing him. The distraction allows Daryl and Michonne to kill their captors while Rick disembowels Carl's captor. In the aftermath, Daryl tells Rick what had happened to him and Beth after the prison assault. Rick then states that the two are brothers. The group makes their way to Terminus, a supposed safe haven. A stealthy infiltration into Terminus still results in the small group being captured. The Terminus crew led by Gareth directs Rick, Daryl, Michonne, and Carl to a boxcar, where they find Glenn, Maggie, Sasha, Bob as well as Sgt. Abraham Ford, Eugene Porter, Rosita Espinosa and Tara Chambler.
In the episode "No Sanctuary", shortly after being captured, the group plots their escape from the train cars as Daryl tells Maggie what happened to Beth. The Terminus crew drops tear gas in from the roof and take Daryl, Rick, Glenn and Bob to a slaughter room where four other survivors have their throats sliced. As Bob fails to reason with Gareth, telling him Eugene has a cure to the walker plague, an explosion caused by Carol and a subsequent invading walker herd distracts Gareth's attention and Rick gets free and kills the two butchers. Rick leads Daryl, Glenn and Bob back to the others where they escape Terminus as it is overrun by a walker herd and begins to burn down. Once outside the group runs into Carol; Daryl runs up to her and hugs her. In the episode "Strangers", the group continues to move along the forest but are distracted by a cry for help from Father Gabriel Stokes, who immediately strikes them all as suspicious after claiming to have not killed any walkers or people, but leads them to his church where they set up shelter. While searching for supplies later, Daryl and Carol find a car and manage to get it working. Daryl sees the car that took Beth drive by, and he and Carol go after it. In the episode "Four Walls and a Roof", the next day, Daryl emerges from the bushes where Michonne asks where Carol is but Daryl tells an unseen person to come out.
Daryl's story is elaborated in the episode "Consumed", when he and Carol discover that cops have taken Beth. They lose track of the cops after their car fails to restart, and nevertheless travel into Atlanta and locate the distinct car again, on top of a parking lot next to the Grady Memorial hospital. While they sneak around and dodge walkers, they encounter Noah, unbeknownst to them a resident and survivor who met Beth. Noah holds them at gunpoint and forces them to surrender their weapons to him. Daryl and Carol comply and are left to deal with walkers freed by Noah to give him enough time to escape. Daryl catches up with Noah eventually and charges him to the ground. A large book shelf collapses on Noah and keeps him trapped while it releases a walker who approaches Noah. Daryl reluctantly complies with Carol's pleas for Noah's life, and Noah shares his story and the whereabouts of Beth. When the group is about to leave the building, two cops hit Carol with their car, seriously injuring her and leaving her unconscious. The cops take Carol away to their post, Grady Memorial Hospital. Noah calms Daryl, saying that they have will take care of her medically. Reluctantly, Daryl vows to return for her with the rest of the survivors, countering Noah's argument that the cops have too much firepower to overwhelm them and Daryl leaves with Noah, revealing that he is the person Daryl brings back to the church.
In the episode "Crossed", Daryl, Rick, Tyreese, Sasha and Noah gear up and head to Atlanta to retrieve Beth and Carol, only to face complications with Officer Dawn Lerner's police subordinates Sergeant Bob Lamson and Officers Shepherd and Lacari. The group captures the three officers and Daryl suggests trading them for Beth and Carol. Eventually, in Coda, the group meets Dawn and her police in the hospital where they traded Lacari and Shepherd for Beth and Carol but when Dawn demanded Noah back Beth stabbed Dawn, prompting her to shoot Beth. Immediately Daryl shoots Dawn in the head before breaking down in tears and soon takes Beth's lifeless body outside, which the rest of the group arrives in time to see.
In the mid-season premiere "What Happened and What's Going On", Daryl is seen standing over Tyreese's funeral. In the episode "Them", two weeks after Beth's death, Daryl is still distraught and appears broken as the group also suffers from dehydration during a drought. Carol tells Daryl that he needs to embrace the pain so he can move on quicker before kissing him on the forehead. Later, Daryl goes into the woods to rest; he smokes a cigarette but then puts it out on his own knuckles, and breaks down in tears. Later, when a storm hits, Daryl leads the group back to a barn he found, where they take shelter. Rick gives a speech about how they need to be dead inside if they want to survive so they can eventually live and calls the group "the walking dead", but Daryl argues that they are not the walkers. Daryl then later talks to Maggie and they help each other with their shared grief. In the episode "The Distance", Daryl pats Aaron down when he first enters the barn. He then agrees with Michonne about going to the community. He rides in the RV during the night, arriving at the flare which Eric fired unharmed. He then takes the RV to Alexandria.
In the episode "Remember", when the group enters the Alexandria Zone, Daryl is extremely cautious about the place and decides not to use any of the amenities they have given him, such as a shower, hence not putting his guard down. When interviewed by Deanna Monroe he refuses to sit down and arrives with his crossbow and a dead possum in his hands, greatly confusing Deanna about what job Daryl could have in the community. In the episode "Forget", Daryl secretly meets with Rick and Carol to discuss the matter of self-defense if things go bad. They kill a walker; Daryl notices a "W" carved into its forehead, leaving them slightly disturbed. Later, when hunting, Daryl runs into Aaron who is also hunting, and they subsequently work together to find a horse Aaron calls "Buttons", which Aaron has been trying to bring back for months. Aaron also notes Daryl's dilemma of fitting in as an outsider, and states that he and Eric feel the same way due to their sexuality. They later see Buttons killed by walkers, and Aaron puts Buttons down before they return. Aaron also encourages Daryl to attend Deanna's welcoming party for Rick's group. Daryl finds himself unable to and instead has dinner with Aaron and Eric before Aaron shows him his garage ful of bike parts, which Daryl can rebuild for himself. Aaron also offers him the job of being Eric's replacement as Alexandria's other recruiter, as he knows that Daryl will always need to be away from Alexandria; Daryl accepts and later, when meeting with Rick and Carol, he questions whether they need to carry hidden guns around and declines to take one. In the episode "Spend", Daryl has finished building his motorcycle, and heads out with Aaron in a car to find more recruits.
Daryl seems to depart from Merle's bigoted outlook throughout seasons 2-5, and in season five he accepts gay characters without comment. He also makes markedly fewer racist or bigoted comments throughout the show, and becomes more trusting of the original group members.
In the episode "Try", outside the walls, Daryl and Aaron notice more walkers are coming into the area. They investigate a light in the distance and come across a woman who had been tied to a tree and eaten alive by walkers. There is a "W" carved into her forehead. In the season finale "Conquer", Daryl and Aaron find evidence of other people moving around the forest and begin to track them. Aaron tells Daryl about how he recruited a group of survivors who were ultimately exiled from Alexandria, and he personally had to escort them out without their weapons. They then see a lone survivor wearing a red poncho in the middle of a field and follow him. They lose track of the survivor and decide to scavenge supplies from some abandoned food trucks. However, they set off a trap set by the Wolves that unleashes a horde of walkers on them and they are forced to take shelter inside a car. Daryl offers to risk his own life to help Aaron escape, but Aaron is adamant that they both escape together. At that moment, a survivor named Morgan arrives and, with his help, Daryl and Aaron are able to escape. They ask Morgan why he helped, and he replies that all life is precious. Aaron offers to bring him to Alexandria, but Morgan politely refuses, saying that he needs to get to Washington, D.C., and shows them the map he picked up in the church, which Daryl recognizes. Daryl, Aaron, and Morgan later arrive back in Alexandria in time to witness Rick execute Pete.
In the season premiere "First Time Again", Daryl talks to Rick about the trap he and Aaron were caught in and the men Morgan encountered in the woods, The Wolves, and Rick is convinced they don't need to look for people anymore and anyone outside has to take care of themselves, but Daryl disagrees, saying that looking for people is how they take care of themselves but accepts that it's Rick's call. When Rick addresses the community about a herd stuck in a quarry nearby, he devises a plan to lure them away from the community and Daryl volunteers to lure them away with his bike, and Sasha and Abraham volunteer to accompany him. As part of the plan, Daryl helps Abraham build a barricade on one of the main roads to prevent the herd from veering off the main road. At the quarry site however, when Rick describes the plan once more for tomorrow, the cliff-side collapses and the trucks keeping the herd contained break free, forcing them the enact the plan immediately instead. As planned, Daryl, Abraham and Sasha manage to lure the herd away from the main road but a siren goes off near Alexandria. In the episode "Thank You", half the herd breaks off and Daryl wants to head back and help Rick but Abraham and Sasha insist he stay, as does Rick over the radio, but Daryl chooses to go back. Eventually Rick radios back and informs them that Glenn, Michonne, Heath, Nicholas, Scott, Annie and David aren't responding and tells them they need to keep going with their plan and Daryl is convinced to head back and rejoin Abraham and Sasha. In the episode "Always Accountable", Daryl encounters a group of people that take him prisoner, and steal his motorcycle and crossbow. He finds a fuel truck and meets back up with Abraham and Sasha.
In the mid-season finale "Start to Finish", a group of men on motorcycles stops the truck and demands all of their possessions in the name of Negan. In the mid-season premiere "No Way Out", Daryl takes out the group with an RPG and he, Sasha and Abraham return to Alexandria in time to rescue Glenn, Maggie and Enid. While Glenn suggests using their fuel truck to draw away the walker horde, Daryl suggests a different plan: getting them all gathered in one place. The group fills the Alexandria pond with fuel from their truck and Daryl ignites it, causing the horde to walk straight into the pond and the fire, killing those the Alexandria residents do not and saving the town. 2 months later, in the episode "The Next World", Daryl and Rick go on a supply run and encounter a man who calls himself Jesus. After a brief altercation, they take the man back to Alexandria. In the episode "Knots Untie", Jesus takes the group to his settlement called The Hilltop, in hopes or trading goods. The group is unsuccessful in coming up with a deal with their leader, Gregory, but he later changes his mind and agrees to give them food if they kill Negan and his men, to which they agree. In the episode "Not Tomorrow Yet", Daryl, along with other members of their group, accompany Rick to a Saviors hideout and murder them, thinking they killed Negan. In the episode "Twice as Far", Daryl, Rosita and Denise go on a supply run to find medicine. On their way back, Denise is killed by Dwight, the same man who Daryl encountered in Always Accountable. After a shootout, Daryl is able to retrieve his crossbow as Dwight and members of the Saviors flee. In "East", Daryl feels blame for Denise's death and goes out to hunt down Dwight, who is unknowingly followed by Glenn, Rosita and Michonne. Glenn, Rosita and Michonne are captured by Dwight, in which Daryl tries to sneak into a small camp set up by the Saviors. He realizes it was an ambush and Dwight shoots Daryl in his shoulder. In the season finale "Last Day on Earth", Rick and his group are captured by a large group of Saviors and are told to kneel down. Daryl, Glenn, Rosita and Michonne are then pulled out of a car and placed beside Rick and the others and forced on their knees. Negan himself then arrives and introduces himself to the group. He demands Rick's group to give him half of everything they have and then states they must be punished for killing his men. Negan then randomly chooses someone from Rick's group and beats to death with Lucille, a baseball bat wrapped in barbed wire.