When Alpha arrives and attracts the attention of walkers, he is forced to rip the knife from his leg to kill the last one, thus opening his wound and losing a lot of blood. In "The Bridge", when Justin pushes Henry after the latter refuses to give him more water to drink, Daryl demands Justin to stop, stating that Henry is just a kid who's doing his job, but Justin reminds him that he's not in charge of the Saviors anymore, so he can't give him orders. She answers that she wants Alpha to suffer for all she's done, but Daryl reminds her that they're not fighting for vengeance, but for their future. Daryl's surprised and asks if he should stay with her. Later, Sherry helps Daryl to escape, and he is helped to Hilltop by Jesus, where Rick and others are meeting to discuss the situation with Negan. Daryl quickly dismisses Richard and the community's theatrics but grudgingly plays along with the group. Daryl and Morgan kill Saviors at various lookout points. She looks on at Maggie tells her people that she wants this to be the last time they do something like this. Daryl mentions someone came through here a while ago. He sets it on the counter beside her and explains that when the Native Americans were being relocated, many of their children died and went missing, and it was believed that the tears of the mothers made a Cherokee Rose bloom. The two have dinner and then Daryl leaves, but before walking away completely he turns around and walks back to hug Carol, telling her to "watch out for herself", again showing great concern for her well-being. Then, they head off in separate directions. At the same time, the group meets a new survivor, In Season 6, he blasts with a RPG a group of Saviors saving Abraham and Sasha. Daryl and Eugene haven't had much interaction on screen, but seem to have a negative relationship due to Eugene siding with the Saviors. Meanwhile, Henry arrives to give water to the workers. He also stated he doubted the flower had grown for his brother, Merle, but instead for Carol's daughter, Sophia. After fighting through a horde of zombies invading Terminus as well as the Terminus residents without his crossbow, Daryl and the others make it back to Boxcar A and set the rest of the group free. A while later, a herd of walkers arrive at the labor site and a commotion ensues. However, Daryl tells Abraham and Sasha that he's leaving them to help defend Alexandria. When Aaron reveals to them that he has been talking with a Whisperer and she has told him the location of Alpha's horde in exchange for seeing her nephew Adam, Daryl orders him to summon a group from Hilltop to help them with the mission before suggesting Carol to stay.

On foot, Daryl chases after Jesus while Rick kills nearby walkers. Together, the two allude to later rectify this error once the Hilltop has time to regroup and fortify. If the Saviors don't surrender, everyone will fight them and he insists that Daryl stick with the plan. Back at the camp, Henry notices an x shaped scar on Daryl's back as he changes his shirt. They check on At the camp, Rick implores his team to find Arat before the Saviors find out and leave, delaying the bridge construction.

Shortly after, Daryl prevents the Whisperer from reanimating and Gabriel offers to help him hide the body. Outside, Henry follows and asks him why a mom would do that to her kid. As Rick descends to the gates, Daryl discreetly arms everyone and lines up a rifle against the gates next to Carl. When Randall was being held in the barn, Daryl brutally interrogated him, and also threatened him and stabbed him in his injured leg in order to obtain information about his group. From afar, Daryl aims his crossbow as the Saviors start accusing him and Anne of being the culprits. Daryl responded, "If you do anything to him-" but gets interrupted by Negan.

Daryl notices Rick's gun on Joey's belt and takes it before hopping on a motorcycle and leaving the compound with Jesus. Daryl is seen in Maggie's office, Dianne reports that they don't have enough ammo to fend off another big attack.

He also directs a large force of Saviors to investigate an explosion set up by the Militia, well-aware that its actually a trap for whoever goes to investigate. As they give her water, Kelly insists to Magna they tell Daryl and Connie about the supplies they've been taking. Carol claims that she didn't have a choice as the Whisperer spotted her, and suggests interrogating him. They deal with the other two quickly, Daryl demanding that Negan untie him once done. Daryl had been very angry and hated the two. Later on, when Rick suggests they camp out on the road, Daryl brings up that Randall reanimated due to a broken neck and wasn't bitten.