It was confirmed on November 19, 2012, that Morgan would be returning in Season 3. In an interview with Inside TV, Robert Kirkman defines the title of the episode "Clear", and how it relates to Morgan: "It means a lot of things. To a certain extent it's the ravings of a lunatic but it's also about him trying to clear out his life and clear out any entanglements around him. He's living by himself so he's trying to have a clear head. It's basically about him getting rid of his wife and getting rid of his son and the only way for him to survive is to clear the area around him." Kirkman also felt that Lennie James was "really playing a completely different character and doing completely different things in this episode and is just as amazing doing it. So it was a lot of fun having him back and also having him do things that were so different from what he had done before." In his recap of the episode for the Los Angeles Times, Todd VanDerWerff called Lennie James a "brilliant actor", and felt that "his role is significant enough that he essentially becomes the main supporting player in the piece". Eric Kain of Forbes called the performance of Lennie James "absolutely riveting", noting that Morgan "is a changed man, and not for the better"; Kain called Morgan's refusal of Rick's offer to return to the prison with him "a glorious scene". Zack Handlen of The A.V. Club describes Morgan's situation: "Morgan's crime is that he couldn't let go of the past; he couldn't shoot his dead wife, and so his dead wife eventually killed his son. So now he has nothing to live for, but he doesn't have the strength of will left to take his own life. Which leaves him trapped. He can't join up with Rick's group, no matter how much Rick wants him to, because that would mean connecting with people again, becoming vulnerable, risking himself and having to suffer when his new friends die. And he can't commit suicide, because that would require a different kind of courage. So he's stuck building his traps, covering the walls with his writing, sending messages to strangers he'll never see."

Lennie James played Morgan in the series premiere "Days Gone Bye". Mike Ryan of Vanity Fair described Morgan in his review of the episode as "scared shitless of zombies breaking in, which seems like a reasonable reaction". Liz Kelly and Jen Chaney of The Washington Post commented on Morgan and Duane, "whose loss of the mother figure in their family reminded us a little of "Lost's" Michael and Walt". Josh Jackson of Paste described Morgan and Duane as being "tormented by Morgan's wife walking the streets outside the suburban home where they're squatting. Unable to put her out of her misery or move on without her, they're frozen in place, tormented by loss that hasn't really gone away. It's the most nightmarish of scenarios – hunted by the shell of a loved one – the zombies aren't generic; this one is personal." Jackson also stated that Rick is "shell-shocked by the world he wakes up to and Morgan serves as his shepherd into reality". Leonard Pierce of The A.V. Club described Morgan as "beautifully played by the always welcome Lennie James" and adding that he "adds a moment of poignancy, as he finds himself actually apologizing for having not killed his now-reanimated wife". Pierce describes the scene in which Morgan "tries to gather the—strength? resolve? compassion?—to destroy what used to be his wife" as a "wrenching" scene. Kris King of Starpulse noted that Morgan "has a powerful scene involving the fate of his wife and his grizzly attempt to come to terms with his loss". Writing for The Atlantic, Scott Meslow describes what he considers "the episode's most devastating scene", in which "Morgan aims at [his wife's] head through a rifle from a window, almost pulling the trigger several times before collapsing in tears. Morgan's fate is a dark reflection of Rick's worst fears; with his wife and son missing, and with no way to contact them, Rick never knows if he'll turn a corner and find a grotesque perversion of the wife and son he loves."

In the season finale "Conquer", Morgan is now in Virginia and sleeping inside of a car, before starting a fire. A man approaches him at gunpoint, revealing himself to be a member of the Wolves, and after a brief conversation, demands that Morgan surrender all of his supplies as well as himself. As another Wolves member lunges at Morgan from behind with a knife, Morgan dodges the attack and fights the men with a wooden staff, overpowering them and knocking them unconscious. Morgan places them in the backseat of the car and blows the horn—checking if any walkers are nearby—before departing. When Daryl Dixon and Aaron become trapped in a van surrounded by walkers when they set off a trap laid by the Wolves, Morgan rescues them and Aaron offers him the chance to come to Alexandria as a thank you for saving them. Morgan initially turns down the offer, but says he is lost but on his way to somewhere, and shows Daryl the map to Washington D.C. with Rick's name on it that he had found at the church. Realizing that Morgan knows Rick, Daryl and Aaron bring him to Alexandria, where they arrive in time to witness Rick executing Pete Anderson under orders from Deanna Monroe following Pete's murder of Deanna's husband.

On November 26, 2017, it was announced on Talking Dead that Lennie James would be exiting The Walking Dead and transitioning the role of Morgan to Fear the Walking Dead.

In the TV series, Morgan saves Rick’s life from a walker and tells him about the outbreak. They part ways with the intention of reuniting in Atlanta but then they lose contact. In the season 3 episode "Clear," Morgan is revealed to be alive when Rick encounters him on a supply run back in Rick's hometown. Morgan has become mentally unstable as Duane was killed by Morgan's undead wife, and refuses to rejoin Rick's group insisting that he needs to stay and clear the town of walkers. In season 5, Morgan is shown to have recovered from his mental break and learns that Rick is in Virginia. He eventually finds the Alexandria Safe-Zone and reunites with his old friend. In season 6 Morgan acts as a man of peace, insisting they can resolve threats without the use of violence, which conflicts with Rick's views, and tries to help him regain his humanity when it continually diminishes. A flashback episode "Here's Not Here" reveals that after encountering Rick the second time, Morgan met a survivor named Eastman who helped him recover from his mental break, teaching him aikido and insisting he doesn't have to kill people no matter the situation.