The episode opens on a country road, with a sign pointing the way for a lost member of someone's group--the kind of reminder of civilization that used to be common in the early days of the series but had all but disappeared recently.
A car is barrelling down the road, with Michonne at the wheel and Rick and Carl riding shotgun and back seat, respectively. They ride in awkward silence until they come upon a man standing in the road, carrying a pack and screaming for help. They speed past him, and find themselves passing a pile-up on the road, where dead and undead bodies alike are found in and under cars.
Trying to avoid the vehicles, Michonne finds herself stuck in the mud; they can't move, and the car is almost immediately set upon by a handful of walkers, including one whose charm bracelet identifies her as "Erin," the person for whom the roadside message was meant.
Cracking the window just a tad, Rick tells Carl to cover his ears and shoots a zombie through the head. Cut to the group on the roadside, no walkers in sight and looking through the belongings of those trapped in the cars. Rick grabs an article of clothing from one of the cars, and wraps sticks and stones in it, creating something to give the car traction. As they're preparing to leave, the man with the pack runs up, screaming for them not to leave him behind, but they do.
During the process, Michonne listens as Carl promises that he's only working with her for the time being, as long as they have the common problem of the Governor to deal with.
Tearing through a small town, the group parks near a series of abandoned storefronts and walks in to scout for supplies. At what looks like the county jail, Rick enters a room that clearly used to be an armory and finds only a few scattered bullets, everything else having been looted.
Rick reveals that this is his police station, from before the plague, and says there are other places to go, but that nothing else will be as good as the armory. Michonne tells Rick that they need an arsenal, and he tells her that the best he'll be able to do is a handful of guns around town that nobody knows are there except him, because he's the one who signed the permits. Michonne hands him a bullet and leaves, and he sticks the bullet in his breast pocket.
Out on the street, Rick sees a giant pile of burned-up walker corpses, and then a series of arrows painted on the ground. They follow the arrows, and find a bizarre set-up, like an obstacle course with inscrutable signs and graffiti all around. As they're working through the obstacle course, though, a walker wanders up behind them and finds herself caught on barbed wire. A sniper, covered head to toe and wearing a helmet, takes out the walker and then demands that Rick and his group drop their weapons, shoes and leave. Rick tells Carl to head for the car, then fires off a couple of shots at the man, who avoids them. Out of bullets, Rick only has the one in his pocket left, and while Michonne heads for the roof, Rick is pinned down. Before the man can fire, though, Carl comes out around a corner and shoots the man down. Rick discovers that the man is wearing body armor, so is unconscious, not dead.
"Do we care?" Michonne asks, and Rick says yes--it's Morgan, the man who saved Rick in the pilot.
With Carl holding a gun on the unconscious Morgan, Rick starts to make his way into the storefronts. He starts to make his way into Morgan's building, and Michonne stops him, warning of booby-traps. Under a welcome mat is a hole that Morgan has apparently sledge-hammered through the pavement. They decide to just bring Morgan home and leave.
Heading up the stairs are more traps, including one at the top of the stairs that leads to an axe at head level.
Inside Morgan's apartment is a giant armory, more than twice what Rick had shown him in the arms locker. Carl and Michonne start to loot his apartment while Rick tries to understand the writing all over Morgan's walls ("Clear," the episode title, recurs over and over again). When Rick leans down to grab a gun, he finds something that shocks him--his old radio, given to Morgan in the pilot. The touchstone to his old life gives him pause, and he sees on the wall the writing "Duane turned." Seeing that, Rick tells Michonne that they're going to wait for him to wake up. Michonne objects, saying that from the traps it's clear he's dangerous, but Rick isn't hearing it. He goes and zip-ties Morgan's hands to await the man's wakeup.
Carl sees a map of the city, scribbled in chalk on Morgan's wall, and goes to study it. Rick asks what he sees, and Carl says that it's their neighborhood, with Rick's house marked as burned. Carl is disappointed to see that it's gone, but says he wants to go find a crib for Judith at a store his mom's friend used to run around the corner. Michonne tells him that she'll go, too, and help him carry the box.
Outside, there are walkers caught up in the traps on the periphery of the neighborhood. Carl tries to shake Michonne, but she tells him she's coming. A walker takes note of them, and Michonne takes it out with her sword; as she does, Carl runs around the corner and almost loses her. When she catches up, he tells her that he wants to do it on his own; she can see the baby store that Carl had alluded to, but he wants to "get Judith something else first," and leaves her.
"I'm sorry this happened to you," Rick tells Morgan (an echo of what he memorably said to the Bicycle Zombie in the pilot), which wakes up Morgan, but he pretends to remain asleep and quietly gets a knife he's got duct-taped to his bed frame.
Rick walks into the other room and lifts a rifle, examining it ; he hears a bullet rattle across the floor and looks back to see Morgan is missing from his bed.
Morgan lunges at him with the knife and, during the scuffle, stabs Rick, babbling about how he doesn't know anyone anymore, that Rick has turned. Rick ultimately ends up with a gun to Morgan's head, and Morgan begs him to kill him.
There's a quick cut to outdoors, where walkers are getting caught in Morgan's elaborate traps, which use animals as bait.
Back inside, Morgan keeps begging for death, with Rick trying to reason with him, and explain to him the story of when they first met. Finally, once Rick shows him the radio and tells him that part of the story, some clarity sneaks into Morgan, who says that he knows who Rick is. He says he tried to reach Rick every day for weeks, first with Duane and then alone. Eventually, he says, after weeks of non-responses, the battery died and there was nothing. His frustration at the memory quickly escalates to an accusatory tone, saying that Rick hadn't been there for him when he tried to reach out. Rick tells him that he kept getting pushed farther out, that he had no choice.
Morgan talks to Rick like his life has been easy, saying that he found his wife and kid and that even once his wife died, since she didn't turn, he didn't have to see that. Then, he realizes that Rick had given him the gun, that he was supposed to have killed her and that he didn't. He tells Rick that one day while scouting for food, Duane had been turned by his mother because Duane couldn't kill her. Morgan killed her--finally--but it was too late for his son.
He asks if Carl is dead, and when Rick says no, he says that he will be--that the good people like Rick and the bad people all die, but for some reason the weak people like him "have inherited the earth."
On the edge of town, Carl and Michonne find themselves outside of a cafe; when Carl tries the door and it won't open, Michonne won't let him go in. After a brief argument, the two agree that Michonne can't stop him from attempting entry, but Carl can't stop her from helping him. They load some caged animals onto skateboards and roll them into the building, where they're set upon by the walkers inside.
With the zombies distracted by the bait, Carl sneaks inside while Michonne stands guard behind him. Carl stands on the bar, removing a framed photo of Rick and Lori that hangs on the wall over it, and an isolated walker reaches up and grabs his ankle; before it can move again, Michonne cuts through its skull and they make a quiet escape toward the door, but a mouse has attracted the crowd of walkers and the two of them end up engaged in a pursuit, wherein Carl takes out a couple of walkers with his gun and Michonne takes out a handful with her sword. Finally they escape onto the street, but Carl has dropped the photo inside. He wants to go in, but Michonne tells him "no more bulls--t," that Carl has to guard the door and she'll get the photo. She returns moments later with the picture, having used Carl's presence at the door to keep the walkers distracted. He tells her that he just thought Judith should know what her mom looked like, and she holds up a small sculpture, saying that she was going to go back in for that anyway.
Back at the apartment, Rick tells Morgan that he's not going to kill him, that he thinks Morgan should come back to the prison with them. He tells Morgan about the prison; Morgan asks if that's where Lori had died. When Rick tells him that the prison is a safe haven where Morgan can heal and get his mind right, Morgan points out that Rick is taking a lot of guns--why does Rick need the guns? He knows that in the world of The Walking Dead, if you've got something good there's someone who wants to take it. Rick tells him that they're going to win, and the Morgan can be there, but Morgan laughs it off.
"You will be torn apart by teeth or bullets," Morgan says, telling Rick that he can't watch it happen anymore. He tells Rick that he's welcome to the guns, but to leave him. Rick tells Morgan that he doesn't accept that this is it for his friend, that Morgan has to be able to come back from this, and Morgan seems to consider it, but still says no.
Outside, Morgan starts piling up dead walkers while Rick takes bags of guns outside; Michonne arrives with Carl and a Pack-N-Play, which they carry around the obstacle course. Before they leave completely, Carl stops to apologize for shooting Morgan, saying that he had to. Morgan tells him not to ever be sorry for doing what he has to do.
Back at the car, Rick asks how things went, and Carl says that things went OK; that he thinks Michonne might be "one of us." Rick seems impressed and stops to contemplate that, when Michonne comes to see him at the back of the car. She asks if he sees something, and says that she knows he sees people--that she used to talk to her dead boyfriend. Rick asks her if she wants to drive, since he sees things, and gives her the keys. They leave town in relative silence but without the same sense of angst in the car; on the way out of town, they see Morgan adding the walkers from his traps onto the pile to be burned.
Passing by the same car accident on the way back to the prison, the group sees the man with the packs torn to pieces at the side of the road, and stops to loot his bags.