In Remember Me, Emerson is asked by Cage Wallace to brief him on the The Woods Clan-Sky People Conflict. Emerson explains that the Outsiders never attacked the Ark as planned and how it is possible they formed an alliance. Later, Cage and Emerson approach the exterior of the Command Center and ask the guard why he is not at his post. Just then, a disguised Monty in a hazmat suit exits the room, giving the all-clear. As he is walking away, Emerson stops him to fill out the log book. Monty fills it out wrong and Emerson tackles him and chokes him out.
In Coup de Grâce, Emerson is on an assassination mission and is spotting for a Mountain Man sniper as they lie concealed in some small scrubs. They watch Clarke riding with Abby and several Grounders on their way from Tondc back to Camp Jaha. The sniper trains his rifle on Clarke just as the group stops briefly. As they are mounting up again, Emerson informs his sniper that he has a shot. Just then, the sniper is struck by an arrow to the neck and killed instantly. The bullet misses Clarke and by chance hits a Grounder near her. Indra and Octavia have found the Mountain Men and Octavia fights Emerson, tearing his radiation suit. Indra tells Octavia to "finish it" just as Clarke rides up and stops her, telling Octavia they want to keep him alive and to check his bag for a patch kit for his suit. Octavia digs through Emerson's bag and finds a picture of Clarke and Lexa on horseback, the intended targets. Indra sends a rider to go warn Lexa of the attempted assassination.
Back at Camp Jaha, Jackson is helping Clarke with Emerson when Raven says she can hook up scrubbers to the airlock to make it safe to take off Emerson's protective outerwear. Clarke tells Abby to let her know when Emerson wakes up. Later, Marcus Kane and Abby are standing watch over an unconscious Emerson. They discuss how the Sky People blood heals the Mountain Men. Abby tells him she is worried about Clarke. Once Emerson wakes up, Kane begins interrogating him but all Emerson will reply back is with his name and rank. Kane threatens to open the door to get Emerson to talk, however, Clarke tells Kane that torture does not work. Kane storms off and Abby puts Emerson under 24-hour guard. Later, Abby tells Clarke and Kane that Jackson found genetic anomalies in Emerson's blood that could have only come from a Sky Person. Clarke wants to kill him but Abby tells Clarke she is not in charge.
After Clarke hears from Bellamy in Mount Weather, she brings Octavia, Indra, and several other Grounders with her to Emerson's airlock where Clarke makes the guard stand down and tells Emerson to get dressed. They take him outside and bring him to the gates where Kane and Abby try to stop her. Abby tells the Camp Jaha Guards to get the prisoner back inside but the Grounders behind Clarke step up threateningly. Clarke tells Abby, "you may be the Chancellor, but I'm in charge," and refuses to back down. Kane tells Abby that it is time they started trusting Clarke. Abby finally gives the order to stand down to the Camp Jaha Guards and Clarke makes her way through with Emerson. She tells Emerson to deliver a message to Mount Weather that they have a secret Grounder army the Acid Fog can't hurt. With the tone generator, they got off of Emerson, the Reapers can't hurt them either. Mount Weather has one last chance to let the Delinquents go and the Sky People will let them live. Clarke then releases air from Emerson's oxygen tank and tells him he has to make the eight-hour walk back to Mount Weather in six hours.
In Rubicon, Emerson is frantically trying to get back to Mount Weather before the oxygen in his tank runs out. He gets to the top of a hill and collapses as his oxygen runs out. Booted feet appear before him and Cage Wallace switches out his oxygen tank. Cage isn't wearing any protection because the bone marrow treatments work and he tells Emerson, "the ground is ours." Once Emerson is back inside Mount Weather, he sits with Cage inside the bone marrow lab. Dr. Tsing drills into a dead Delinquent and extracts bone marrow to give to Emerson. Cage asks Emerson about Clarke and Emerson gives him the message that they're supposed to release the Delinquents. Cage then tells Emerson that it doesn't matter because that night, he's going to drop a missile on Tondc where all of their leaders are meeting. Meanwhile, Bellamy is hiding in an air duct and overhears everything they have said.
Later, in the Mount Weather Command Center, Emerson asks Cage for his authorization code to arm the missile. The missile is armed and ready to go as Cage and Emerson enter the coordinates provided to them by Whitman, their spotter in Tondc. Cage then gives the command to fire the missile and Emerson presses the key to launch the missile on Tondc.
When Cage confronts his father about the radiation leak on Level 5, Emerson enters with some Mount Weather Guards. They force Dante to have the marrow treatment that will allow him to be safe from radiation in 48 hours.
In Resurrection, Outside the Delinquents' dorm, there is an explosion in the hallway as Mountain Men come without any guns because they need the Delinquents alive. Some of the Mountain Men, including Emerson, aren't wearing hazmat suits because they've been cured by the bone marrow of the Delinquents. The guards bust down the door and throw in knockout gas before pulling down the furniture the Delinquents had stacked up in front of the door. They enter the Mess Hall to find all of the Delinquents passed out on the floor. Emerson removes his gas mask and sees a bucket of water with the knock-out bombs soaking inside. He turns around, realizing the Delinquents are faking it just as Jasper rises up, screaming, "NOW!" All of the Delinquents jump up and begin brutally and desperately attacking the guards, hacking and beating 10 of them to death. Emerson screams for his surviving men to retreat and starts pulling his men to safety as they run out of the room.
Later, Emerson and Cage Wallace approach Maya, looking for her. They force Maya in a hazmat suit onto Level 5 as Cage tells the Delinquents she only has 20 minutes of oxygen in her suit so Jasper only has 20 minutes to save her by surrendering. After 30 minutes, Cage and Emerson are walking toward Level 5 saying that the Delinquents had made their choice and Cage orders the guards (who now have guns) to go in strong and take them alive, if possible. This time, they throw flash-bangs through the blockade into the Mess Hall and then storm inside. Emerson calls for Cage and Cage walks in to find the Mess Hall completely empty. He orders his guards to find the missing Delinquents.
In Bodyguard of Lies, in Mount Weather, Emerson enters the Command Center and Cage Wallace asks to be briefed on the remaining 44 Delinquents who have disappeared. Emerson tells Cage that he has people going from room to room looking for them. Emerson tells him there are people inside Mount Weather who don't agree morally with what they're doing to the Delinquents. They discuss using the fact that the Delinquents irradiated an entire level killing 10 of their soldiers and Dr. Tsing to flush them out. They then discuss the Grounder army stopped just outside The Veil's range and Cage wants to know why. Emerson tells Cage that, "this commander is different."
Later, it is revealed that Cage and Emerson have intercepted Bellamy's radio signal to Camp Jaha. They have allowed Bellamy to think he had disabled the Acid Fog machine before they cut his communication with Raven. Cage has the Acid Fog panel reset while Emerson sends guards to capture and bring back the intruder. After the Acid Fog panel is reset, Cage tells Emerson to wait 10 more seconds before deploying the Acid Fog because he wants to make sure all of the Grounder army is inside the kill box as the army continues to march closer. When Emerson counts down to One, Cage says, "we're go for Veil." The Acid Fog machine starts to fire up before a massive explosion takes place, blowing out everyone and everything in the Acid Fog room and traveling through the air ducts. Emerson tells Cage the Acid Fog didn't work and that there was an explosion in the Acid Fog room. Emerson says that the Reapers can't take on a force that large and Cage gets upset, asking what else they have. Emerson admits they have nothing but the door left.
In Blood Must Have Blood (Part 1), Cage Wallace comes over the Mount Weather PA, announcing to all of the citizens that they can return to the ground. He tells them that before the Delinquents murdered her, Dr. Tsing had found a cure in their bone marrow. He asks for the residents of Mount Weather to turn over the "44 murderers" and if they don't, they will be considered enemies. After Cage hangs up the PA, Emerson tells him that there is nothing they can do about the Grounder army marching on them from outside because their Veil is down and the army is too close for missiles. Cage tells Emerson that as long as they are behind the doors, the Grounders can't touch them. He then gets upset that Emerson hasn't found Bellamy, the intruder, yet and throws some papers around, telling Emerson to go door-to-door to find him and the still-missing Delinquents.
When the power goes out all over Mount Weather, Cage tells Emerson over radio to start the clock for one minute. Emerson tells Cage he is not letting the Grounders get near the door. When the light over the door goes off, Sgt. Miller tells Clarke they have one minute to blow the lock. Clarke and Lexa hold the trigger and press the button together but nothing happens. Clarke realizes that Mount Weather is jamming the trigger signal and tries to get closer. As she starts to approach the door, gunfire rains down from above as Emerson and his men shoot at them from the ridge above the door, preventing them from getting closer. A group of Grounders create a shield to take Sgt. Miller to the door so he can trigger it manually. They are all shot down before they can make it. They only have a few seconds left when Lincoln comes up with the idea to use a flaming arrow to trigger the bomb on the door. He makes the shot with only a second to spare and the lock is blown. Lexa tells Lincoln to remain with Clarke while she takes a group up the ridge to take down Emerson's contingent so they can work on getting the door open.
Once the shooting from the ridge has stopped, the Grounder army is able to get the door open. Clarke gives the command to attack just as Lexa interrupts telling them all to stand down. Lexa arrives from the ridge, towing Emerson along just as through the open door, harvested Grounders start stumbling out. Clarke asks if that means the Mountain Men have surrendered and Emerson says, "not quite." Clarke asks Lexa what she did and Lexa tells her she saved her people but Clarke's people were not part of the deal. Emerson then heads back inside Mount Weather as the last of the Grounders are released.
In Blood Must Have Blood (Part 2), in Mount Weather, Cage Wallace is told he is needed in the dorm where all of the Sky People are tied up as they extract bone marrow from a Delinquent. Emerson tells Cage that they suffered losses and he is the only one left who has received the bone marrow treatment. Emerson then reveals they've captured four additional Sky People outside the Mountain: Monroe, Sgt. Miller, Abby, and Marcus Kane.
In the Command Center, Clarke spots Emerson on video in the Mess Hall. She calls him over the radio and tells him to give the radio to Cage. Clarke tells Cage she has his father and tells him she'll kill Dante Wallace if he doesn't let her people go. Cage orders Emerson to go to the Command Center and kill them. Bellamy asks Monty to deactivate Emerson's key card. Clarke tells Monty to get it set up so they can irradiate Level 5 if they have to. Monty finishes the settings to irradiate Level 5 as Emerson gets ready to blow the door to the Command Center. Clarke reaches for the lever and Bellamy places his hand on top of hers, saying, "together," and they pull the lever. The Mount Weather residents begin to succumb to the radiation as alarms go off. Emerson realizes what they have done and takes off running, clearly shaken.