Fifty-six years ago, when the Mountain Men first discovered the Outsiders were able to walk above ground, they began conducting experiments on them. Through the use of the Cerberus Project, the Mountain Men would collect Grounders using the vicious Reapers they created. Then through the Harvest Project, the Mountain Men would use the Grounders to help filter the radiation out from the Mountain Men's blood.
They eventually progressed onto using the Sky People's bone marrow, leading to all-out war and later the irradiation of Mount Weather by the Sky People.
In The Calm, Monty is kidnapped by Mountain Men, unbeknownst to the rest of the Delinquents.
In We Are Grounders (Part 2), the Mountain Men storm the camp of the Delinquents, taking in the remaining amount from the battle with the Woods Clan. Clarke wakes up in quarantine, only to find herself locked in a room across from Monty. She sees a sign that says Mount Weather on it and looks on in fear.
In The 48, Clarke is still trapped in the white room. She looks across the hall and finds the room where Monty was before is empty and sees a person in a hazmat suit. Clarke breaks out of the room and takes the girl in the hazmat suit hostage demanding to see her friends. Clarke reaches level 5 and the mess hall and before a Mount Weather citizen alerts the others of a containment breach and Clarke is knocked out by guards. Clarke later awakes in medical and introduced to Dr. Tsing and Dante Wallace, Clarke again demands that she see her people and Dante Wallace allows her to, bringing her to the mess hall. There, Clarke is reunited with Jasper and Monty. Later, during a meal Monty and Jasper are trying to convince Clarke to try the various food but Clarke refuses to eat Mount Weather's food and claims everything is too good to be true. Jasper leaves her and goes to find more chocolate cake and is offered some by a girl named Maya, the same girl Clarke took as a hostage at the beginning of the episode. Clarke approaches them and apologizes to Maya, however, she takes her keycard. Clarke searches for an exit and finally finds one but is pursued by Jasper and Maya. Clarke prepares to pull the lever but Jasper tells her that if she does, everyone in the Mountain will die so Clarke doesn't pull the lever and is taken by guards. At the end of the episode, Clarke enters the dorm and finds a box of oil pastels on her bunk from Dante Wallace in order to foster trust. At dinner that night, Clarke finally eats their food and is filled with temporary contentment.
In Inclement Weather, Clarke is in the Mount Weather dorms adding details to the map she has been given. Jasper is chatting with Maya before an alarm goes off alerting her that a patient needs medical attention. Maya leaves and Clarke follows her, Jasper following Clarke in turn. They enter quarantine and find a dead Mount Weather Guard with a wound. Dr. Tsing orders that they leave just as another patient who is covered in radiation burns is brought in. Clarke is later in the mess hall and she tells Jasper that Sgt. Shaws wound looked like a gunshot wound and that since grounders don't use guns, Ark survivors must be on Earth. She meets with Dante Wallace and requests that she see Shaw's body. Dante grants her request and brings her into quarantine where she sees Shaw's body. Dr. Tsing allows her to see the exit wound and Clarke realizes, it does indeed look like an arrow wound. She is talking to Jasper later and he tells Clarke that maybe it is an arrow wound and she needs to stop being so skeptical and appreciate the fact that they are safe now. Clarke glances across the mess hall and sees a Mount Weather guard, the same one who arrived with radiation burns earlier and he seems entirely cured. Clarke follows him but is taken away since only patients are allowed in medical. Determined to get into medical, Clarke opens her stitches. She later awakens in medical and sees the same guard on a bed having blood circulated through his body. Clarke follows the tubing and enters the Harvest Chamber and is horrified to see hundreds of grounders in cages being drained for their blood. She rushes towards one of the cages and sees Anya is a prisoner in the mountain as well.
In Reapercussions, Clarke and Anya spend the duration of the episode escaping the Mountain. Anya at first refuses to help Clarke and goes off in her own direction forcing Clarke to follow. They are soon corned by reapers which the Mount Wheather Guards kill before taking Clarke. She tells them she knows what they are doing to grounders and they remark she'll be put in the Harvest Chamber with them. However, Anya saves her by taking off the helmets of the men's radiation suits, killing them. Anya tells Clarke she's found an exit which happens to be over a dam. Clarke hesitates then jumps off the dam, following Anya. Jasper is seen with Maya in the Art Warehouse however, they are forced to leave upon noticing guards. They encounter Monty who expresses worry about Clarke but Jasper brushes him off. Later, Jasper approaches Monty in the Mess Hall and Monty again expresses worry over Clarke. He mentions that Clarke didn't trust the Mountain Men but Jasper assures him he thinks they can trust Maya. Maya then approaches them and tells them Clarke had a breakdown and is in the psych ward being monitored. Jasper expresses worry over Clarke and regrets the fact that he had called her crazy just the day before as Maya comforts him and promises to get him more information.
In Many Happy Returns, Clarke convinces Anya they need each other to defeat Mount Weather. However, just after Anya finally agrees she is shot by a Camp Jaha guard and ends up dying.
In Human Trials, Clarke is brought into Camp Jaha after being mistaken for a grounder prisoner. Abby immediately recognizes Clarke and has her released. After Clarke's wounds are treated Major Byrne asks her where she's been to which Clarke explains she's been held captive in Mount Weather by the Mountain Men, and they need to get the other's out. Later, at a council meeting, Sinclair, Major Byrne, and Chancellor Griffin decide to gather intel on Mount Weather before sending out a rescue mission. Inside the Mountain, Dante meets with Jasper and tells him that Clarke ran away. He offers Jasper a chance to go after her and Jasper at first agrees. He returns to the dorm and tells Monty who is determined to go after Clarke. Maya enters the dorm and tells Jasper he can't leave as it isn't safe. Jasper tells Maya that Clarke would do the same for him and questions why he's so scared. Suddenly, alarms begin blaring and Maya begins to develop radiation blisters informing Jasper and Monty there is a containment breach. Jasper and Monty accompany Maya to quarantine and Dr. Tsing informs them the only way to save Maya would be to circulate her blood through their system. Jasper volunteers and the experiment is performed. The experiment is a success and Maya wakes up to be told by Dr. Tsing that Jasper saved her life. Dr. Tsing then goes to meet with Cage Wallace and Dante. She informs them that the first human trial was a success and she needs permission to move forward with the rest of the 47. Dante declines this. Throughout the duration of the episode, Cage is also turning Lincoln into a reaper. He injects him the red drug so that Lincoln develops an addiction and eventually kills another grounder to be awarded another dose.
Lexa commands her people to stand down and retreat after negotiating a truce with the Mountain Men that allowed the release of her people. When the Grounders retreat, almost all Sky People accept defeat and soon retreat.
Clarke has Monty hack into Mount Weather's air filtration system, and she and Bellamy irradiate the mountain, eradicating the population.
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After the irradiation of Mount Weather, only two Mountain Men who had received the marrow treatment survived: Cage Wallace and Carl Emerson. As Cage tried to escape through the woods, he encountered Lincoln, whom he had turned into a Reaper once before. Lincoln kills Cage, leaving Carl Emerson as the sole survivor.
Three months after the war, several dozen Sky People moved into Mount Weather. However, Emerson had told the Ice Nation how to activate the self-destruct mechanism for Mount Weather. The Ice Nation sent an assassin who successfully blew up Mount Weather, killing 49 Sky People inside, 35 of whom were from Farm Station. This led to the Ice Nation Queen, Nia, being brought in for treason and eventually killed by Lexa. Roan, the new king of the Ice Nation, captured Emerson and sent him to Clarke and Lexa. Instead of killing him, Clarke chose for him to be banished.
Later when Clarke and a group of others returned to and abandoned Arkadia, Emerson appears disguised as a grounder systematically capturing each member roaming around Arkadia. During this process, Emerson ended up killing Sinclair by mistake. Clarke and Bellamy being the only ones not captured, go after Emerson and find him holding everyone captive. Emerson had Bellamy turn himself in, then Emerson grabs Clarke. Emerson sealed the door with everyone inside of the room, cutting off the oxygen, to make Clarke feel what he felt. Clarke fought to free her friends, but Emerson managed to take her down to make her watch everyone die. Clarke, however, surprised Emerson with A.L.I.E. 2.0, and the AI entered Emerson neck, causing him to bleed out of his eyes, nose and neck, killing him. Clarke freed her friends from captivity, and the last Mountain Men was finally dead.
Clarke: "I've been thinking about Mount Weather. How come they didn't attack until Jasper crossed the river? It's not like we were being quiet and they didn't know we were there. They waited for us to cross. The river's a boundary. Which means Mount Weather is off limits."
Dante: "My father, this was his office at the time, believed it meant that the Earth was survivable again, and so, he opened the doors. Within a week, 54 people were dead from the exposure. My mother and sister among them."
Clarke: "I'm letting you go. I'm not weak, but I'm not like you. Our only chance against Mount Weather is if we fight together. To beat them, we'll need our technology and your knowledge of this world. I know my people will help. The question is, will yours?"
Anya: "The commander was my second. I can get an audience."
Raven: "I tweaked the resonator and got this. It's on every frequency. Long-range communication is totally screwed. It's also why the range in our walkies sucks. It's the same signal Monty heard on the black box of the Exodus Ship. Mount Weather crashed the exodus ship."
Bellamy: "I needed to know what happened after the intake door."
Lincoln: "They remove your clothes, blast you with boiling water, and douse you with something that burns even worse. From there, we were sorted. The others were tagged Harvest. I was tagged Cerberus, turned into a Reaper."
Bellamy: "Cerberus. Three-headed dog that guards the underworld"
Lexa: "Its also our only choice and you know it. You could've warned everyone out there but you didn't. You said nothing, not even to your own people. This is war Clarke, people die. You showed true strength today, don't let emotions stop you now. It's time to go."
Clarke (to Octavia): "I did it to save Bellamy, so that we could win this war. Don't you see that? If we'd evacuated Tondc, Mount Weather would've known that someone tipped us off. They would have found your brother."
Clarke: "This is a rescue mission. We are not here to wipe them out. There are people inside that mountain that have helped us, children, who have nothing to do with this war. We kill their soldiers, their leadership if we have to, but we are there to rescue our people. Is that clear?
"There are 4 teams. Two of them at the dam and in the mine are moving into position already. The third inside the mountain is freeing the Grounder prisoners as we speak. It is our job as the fourth team to keep the eyes of the enemy off of them for as long as possible. To do that, we have to be in position here at the main door with our entire army. The Mountain Men believe the door can't be opened from the outside, so they leave it unguarded. Only it can be, and thanks to our source on the inside, now we know how."