In Long Into an Abyss, the pair first meet when Clarke goes to Lexa's tent to make her an offer. When Lexa first sees Clarke she immediately recognizes her as the girl who burned three hundred of her warriors alive, however, Clarke points out that Lexa was the one who sent the three hundred warriors to kill the Delinquents. Clarke admits that she has come to make a deal but Lexa says that the issue isn't negotiable, however, when Clarke says she knows how to beat the Mountain Men Lexa allows Clarke to say what she wants to say. Clarke explains the Harvest Chamber to Lexa and explains that she managed to escape Mount Weather with Anya. Clarke also gives Lexa a piece of Anya's hair and offers her condolences. Lexa wonders if Anya died well and Clarke reassures Lexa that Anya died by her side trying to get a message to Lexa; the only way to take down Mount Weather is if both groups join together. Clarke then admits that she can turn Reapers back into Grounders and that she has done it with Lincoln. Lexa demands Clarke to show her Lincoln as proof. Clarke takes Lexa, as well as a few other Grounders, to the dropship. However, when they arrive they find out that Abby had failed at saving Lincoln. Lexa accuses Clarke of lying and tells her that the time given for the Sky People to leave Camp Jaha is up, and then proceeds to give her fellow Grounders permission to kill everyone in the dropship. Just as everyone prepares to fight, Abby manages to shock Lincoln and restart his heart. Lexa calls off her Grounders and leaves the dropship with them once she sees that Clarke was telling the truth. Later, Lexa and Clarke talk in Lexa's tent once again. Lexa admits that she is very impressed with Clarke being able to bring back Reapers, however, she says she needs one last thing before the truce between the Sky People and Grounders can take place. Clarke says she will do anything. Lexa says that she needs Finn in return for a truce since he was the one who created the massacre. Clarke is left speechless and shocked at the demand.
In Spacewalker, after Finn hands himself over to the Grounders, Clarke goes to see Lexa before his execution. Lexa tells Clarke that she cannot stop Finn from dying. Clarke agrees and points out that Lexa can, though. Clarke wants Lexa to show the Sky People how powerful she is and show them that she can be merciful by letting Finn go. Clarke wants Lexa to show the Sky People that the Grounders are not savages but Lexa just says "We are what we are". Clarke then tries to get Lexa to kill her instead of Finn and lists all the bad things that she has done to Lexa's people, however, Lexa points out that Finn is the guilty one. Clarke argues with Lexa and points out that Finn is not guilty because he did it for her. Lexa just tells Clarke "Then, he dies for you". Clarke realizes that the attempt to convince Lexa to let Finn go is hopeless so she asks to say goodbye to Finn and Lexa allows this. Clarke then mercy-kills Finn, stopping the Grounders from torturing him to death, and leaving Lexa shocked. The other Grounders try to charge at Clarke, however, Lexa calls them off.
In Remember Me, Lexa tells Clarke that even though some of her people are not satisfied with Clarke mercy-killing Finn, she knows that Clarke's suffering will be much worse. Lexa then tells Clarke that Finn's body needs to be taken back to Tondc so a death ritual can be performed. Clarke agrees to this and Lexa allows her to choose some people to bring along. During the death ritual, Lexa allows Clarke to be the one to set fire to Finn's body. Lexa is impressed when Clarke says "Your fight is over" in Trigedasleng seconds before lighting Finn's body on fire. Later on, Lexa opens up to Clarke about having lost a lover, too. Her name was Costia and she was tortured and killed by the Ice Nation. Lexa then tells Clarke that she thought she would never get over the pain but eventually did. Clarke wonders how Lexa did it and then Lexa says she just realized what it really was; weakness. Lexa tells Clarke that she stopped loving and caring for people since "love is weakness". Clarke admits that she could never do that but Lexa tells her that if she doesn't stop she will put the people she cares about in danger and then walks away. When the Sky People are accused of poisoning Gustus Clarke denies it, however, Lexa believes that when Clarke plunged the knife into Finn's heart, part of her wished it was Lexa's heart. Clarke realizes that it was one of Lexa's Grounders who poisoned Gustus because the poison was in the cup, which he drank from, and not the bottle that was given to Lexa as a gift. Clarke proves it to Lexa by drinking from the bottle. Bellamy accuses Gustus of poisoning himself but Lexa says he would never hurt her, but Bellamy points out that Lexa was not the target; the alliance was. Clarke tells Lexa that she knows it wasn't one of the Sky People. Gustus admits he did it and is then executed for it, with Lexa delivering the final blow. Later on, Clarke appears to set aside her guilt regarding Finn's death, walking up to her persistent hallucination of him and stating "Love is weakness," hardening her heart, just as Lexa had done, and is then seen returning to the war room with Lexa.
In Survival of the Fittest, Lexa and Clarke, along with numerous other Grounders, are planning their war with the Mountain Men. Throughout the planning, a Grounder named Quint tries to start trouble with Clarke because she burned his brother alive in a "ring of fire." Lexa forces Quint to stand down and he eventually does, however, Quint later attempts to kill Clarke while she is out in the woods, "getting some air." Lexa saves Clarke's life by stabbing Quint in the hand with her knife and gives Clarke the opportunity to kill Quint. However, Clarke hesitates and then distant growls are heard. Lexa seems to recognize the creature by its growls and tells Clarke and her Grounder guard to run. Lexa stabs Quint in the leg and allows him to be killed by the creature as a distraction, buying them some time to flee. Later, the three try to fight off the giant gorilla. Lexa's guard is killed, leaving only Lexa and Clarke alive. The gorilla grabs hold of Lexa but Clarke shoots the gorilla repeatedly, forcing it to let go. The pair manages to hide. Clarke tends to Lexa's injury and Lexa chastises Clarke for not leaving her to die, calling it weakness. Clarke then informs Lexa that she saved her because she is absolutely necessary for the success of their alliance. The gorilla finds them again and tries to get inside the cage where Lexa and Clarke are hiding, however, Clarke opens the doors and allows it to run in. After the gorilla is inside, both Lexa and Clarke immediately run outside and lock the cage door. Clarke wakes up near Lexa and a campfire and hears the gorilla growling but Lexa assures Clarke that she is safe. As they are about to leave, Lexa stops Clarke and tells her that she was wrong and that Clarke's heart shows no sign of weakness. Clarke realizes how to take down Mount Weather. She explains to Lexa that the army is already inside of Mount Weather and they just need to be let out.
In Coup de Grâce, Clarke and Lexa are seen in a photograph together that was taken by the Mountain Men. Both Lexa and Clarke are the targets of the Mountain Men.
In Rubicon, Clarke heads to Tondc to warn Lexa about the missile that the Mountain Men are planning to launch at the village where the leaders from all twelve Grounder Clans will be. Clarke wants to evacuate Tondc but Lexa disagrees and explains to Clarke that if they evacuate the village the Mountain Men will know that there is a spy inside Mount Weather, and Bellamy's cover will be blown. Clarke argues that it's wrong to leave the people to die by the missile, but Lexa tells Clarke that they are at war and in war people die. Lexa points out that Clarke already knows this and that is why she did not warn any of her people when she was given the chance. They ultimately agree to sacrifice the village. The pair are in the woods when Clarke sees her mother. Lexa warns Clarke that there isn't enough time, but Clarke goes back to get Abby and leads her into the woods. The missile finally hits Tondc and causes a massive explosion, and multiple people are killed.
In Resurrection, Lexa finds Clarke on the outskirts of Tondc, in a daze. Clarke tells Lexa that she "could've warned them" and shows much remorse for leaving the people of Tondc to die. Clarke wants to go back and help them, however, Lexa points out that there is a sniper in the woods from Mount Weather, and Lexa argues that the Mountain Men might fire another missile if they see that Clarke and Lexa have survived. Clarke says she isn't going to let the sniper tell the Mountain Men that they survived the attack because she is going to kill him. The pair later meet up with Lincoln in the woods. The three of them continue after the sniper. In the morning, the group finds the sniper and he tries to kill all three of them, however, Clarke shoots him through Lincoln's shoulder as he holds a knife to Lincoln's throat. The three make their way back to camp. Lexa tells her people that "the dead will be avenged!", and she and Clarke begin making their way to Mount Weather, along with the Grounder warriors.
In Bodyguard of Lies, Clarke and Lexa are in Lexa's tent, waiting for the signal that tells them that Bellamy took care of the Acidic Fog. Lexa is shown lying on her bed while Clarke is hovering over maps, worrying about the upcoming battle. Lexa tells her battle plans don't last long in battle and they can't move forward until the Acidic Fog is disabled. She tells Clarke that she's doing the same as she did when she first took command, over thinking things while not being able to move forward. When Clarke expresses concern about Bellamy, wondering if she sent him to Mount Weather to die, Lexa shows some jealousy when she realizes Clarke cares for him. Lexa then says to Clarke that sometimes they have to look into the eyes of their warriors and tell them to "Go die for me". She tells Clarke that she "could be a leader your people look to. Pour their hopes and dreams into. Someone they will fight and die for." Clarke says she never asked for that and that she's just trying to keep them alive. Lexa then tells Clarke that she was born to be a leader, just like she was.
Lexa overhears Octavia confront Clarke about the missile. Clarke reassures Lexa that Octavia won't say anything to anyone, but Lexa points out that they cannot be sure. When Clarke leaves, Lexa orders one of her Grounders to go and kill Octavia. Once Clarke finds out that Lexa ordered another one of the Grounders to kill Octavia, she stops the Grounder from killing her and drags him back to Lexa's tent. Clarke is furious at Lexa. She tells Lexa that she cannot just kill anyone she distrusts, but Lexa claims she can. Lexa tries to make Clarke see that Octavia is a threat and if Clarke wasn't so close to Octavia she would be able to see that. However, Clarke argues that it's because she's close to Octavia that she knows she is loyal and never would expose the truth. Clarke also tells Lexa she has changed and can't risk the lives of her people anymore. Lexa wonders if Clarke is willing to risk everything on her feelings and Clarke says she will. Clarke then proceeds to call Lexa a liar because she hides her feelings. Clarke tells her that she "felt something for Gustus" and is "still haunted by Costia". Clarke says she can see right through Lexa. Lexa orders her to leave, but Clarke ignored this and also tells Lexa that even though she felt something for the two-hundred and fifty people in Tondc, she let them burn. Clarke does all this while advancing on Lexa, actually causing the Commander to take several steps back until Clarke corners her by a table. Lexa points out that she didn't let everyone die and tells Clarke that she didn't let her die. Clarke realizes that Lexa cares about her. Clarke says for Lexa to trust her but she says she can't. Before Clarke leaves, she says that if Octavia is harmed in any way she will tell everyone that they knew about the missile. After Clarke leaves, Lexa is shown to be affected and upset by her words.
Lexa calls Clarke to her tent and explains to her that Octavia doesn't have to fear her anymore and tells Clarke that she does trust her. Clarke thanks Lexa, understanding how hard it is for Lexa to trust her. Lexa says that even though Clarke thinks her ways are harsh, it's how she, and her people, survive. Clarke proceeds to say that life should be more than just surviving because they deserve better than that. Lexa agrees and kisses Clarke. Clarke kisses Lexa back and the kiss is long and passionate. Eventually, Clarke pulls away because she's not ready "to be with anyone" so soon after Finn's death. However, Clarke adds "not yet" and that gives Lexa hope that a relationship may happen in the future. Lexa gives Clarke a nod, showing she understands why she needs time.
After the Acidic Fog is disabled, the two head outside to signal the rest of their warriors into battle. They are then seen walking side by side in the woods with the entire army behind them. They share another look at each other, before charging into battle with the rest of their army.
In Blood Must Have Blood (Part 1), Clarke, along with some other Sky People, meet in Lexa's tent with some of her people. They review the plan to take down Mount Weather and begin chanting "Blood must have blood" in Trigedasleng. While at Mount Weather's door, Lexa asks Clarke what she is planning on doing after the battle, but Clarke says she doesn't know. Lexa asks her to come to Polis with her because it will change the way she looks at things, but Clarke points out that Lexa already has done that. The two press the button together that is supposed to explode Mount Weather's door, however, nothing happens. Later on, the Grounders and Sky People manage to get the door pulled open and Clarke gives them the signal to attack, however, Lexa stops them. Clarke rushes over to Lexa and sees Emerson is with her, and wonders what is going on. When Clarke sees the Grounders from the Harvest Chamber exiting Mount Weather, she believes that the Mountain Men are surrendering, but Emerson says "Not quite". Lexa admits she made a deal with the Mountain Men; they will release her people and leave them alone for good as long as she lets them kill the Sky People for their bone marrow. Clarke is upset by this and says that Lexa doesn't care, but Lexa says she does care and that it's what she would have done for her own people, too. Clarke watches as Lexa orders some of her guards to take Lincoln as a prisoner and orders another guardsman to sound the retreat, letting Emerson go. Once the Grounders leave, Clarke is left upset and shocked by Lexa's betrayal.
Lexa and Clarke reunite in Wanheda (Part 2) as Lexa had ordered Roan to bring her "Wanheda" so Clarke wouldn't fall at the hands of the Ice Queen. Lexa is angered that Clarke is presented to her injured, to which Roan replies that she didn't come easily, as Lexa expected. Lexa informs Clarke that a war is brewing and that she needs her to which Clarke spits in her face and proceeds to yell death threats as guards drag her out of the room.
In Ye Who Enter Here, a week has passed and Lexa has obeyed Clarke's wishes to be left alone, but tells Clarke that more pressing matters have come up. Lexa says that she is hosting a summit with the Sky People at sundown and that she will be returned to her people. Clarke questions why Lexa captured her just to return her to her people but Lexa says she saved her. Clarke retorts and says she could have used saving back on the mountain. Lexa then asks Clarke if she would have done something different if she had been offered the deal. Clarke says she wouldn't have betrayed her friends, but Lexa says she did by killing everyone in the Mountain. Clarke believes that Lexa is also at fault for the massacre but the difference between them being that Lexa has no honor and Clarke had no choice. Lexa then tells Clarke she wants the Sky People to become the 13th clan and that way, no one would dare make a move on them as they would be making a move on her. Clarke refuses and says that she knows everything Lexa has done thus far was to protect her power over the Coalition. As the events in Mount Weather made Lexa look weak, and her existence as the Wanheda compromises Lexa's influence even further. Clarke tells Lexa that she will never bow to her; and further adds that if Lexa wants her power, then Lexa must kill her and take it--otherwise she can float herself.
After her talk with Roan, Clarke asks for Lexa. When she comes to her room, Clarke attacks her with a knife and holds it against her throat. However, she hesitates when Lexa makes no effort to defend herself and instead looks into Clarke's eyes and quietly whispers "I'm sorry". Clarke pushes Lexa away in tears while turning away and drops the knife as Lexa says she never meant to turn her into this. She tells her that she's free to go and she'll escort her to her mother. Clarke stops her and accepts Lexa's previous deal.
Later that night, Clarke enters the throne room for the ceremony. Lexa tells everyone that the reason for the summit has changed and the Sky People will be joining the Coalition. As Kane is getting branded on behalf of the Sky People, Bellamy, Octavia and Pike burst in before realizing that Echo tricked them. When Lexa's leadership is threatened, Lexa considers the attack an act of war and orders everyone from the Ice Nation arrested and allows Kane, Abby, and Indra to head to Arkadia. When Lexa says that they need an ambassador from the 13th clan to stay, Bellamy tries to argue that it's not safe for Clarke but Lexa says she will be under her protection.
Later, Clarke is contemplating how the Ice Nation knew of the self-destruct mechanism in Mount Weather and Lexa says they'll figure it soon and thanks Clarke for staying. Clarke says that she stayed because it was the best thing for her people, which Lexa then corrects to "our people". Clarke warns Lexa not to betray her again and Lexa says that she won't as she gets down on one knee. Lexa then vows fealty to Clarke, swearing to treat Clarke's needs as her own and her people as her own. Clarke takes Lexa's hand, accepting the proposal.
In Watch the Thrones, Clarke is attending a meeting with the ambassadors the 13 clans. Guards bring Nia in who was responsible for the destruction of Mount Weather. Lexa tells Clarke that Nia has been charged for crimes against her people and Clarke demands justice. Nia, however, attempts a coup and when the vote isn't unanimous due to Clarke not supporting it she issues a challenge against Lexa. She chooses Roan to be her champion and when Lexa is asked who will be her champion Lexa says that as heda, no one fights for her.
Clarke meets with Lexa later and begs her not to go through with the match but Lexa refuses saying that she should die today her spirit will choose its successor, something Clarke needs to accept. Clarke tells her she won't just sit there and watch Lexa die and decides to not attend the match. She meets with Roan in the Polis marketplace and begs him not to go through with the match and offers him a chance to become kind of Azegeda. Roan refuses to do it himself but offers to let Clarke do it.
Clarke goes to Nia and lies saying she shall ally with her before beginning the blood oath. However, Ontari, who is guarding Nia, realizes it is a trick and Clarke is trying to poison her. Nia drips some of Ontari's blood onto Clarke's face as a message for Lexa. Clarke is shocked and tells Lexa she's never seen blood that color before and Lexa explains that it is nightblood, the blood of the commanders. Later, Clarke attends Lexa's match. Lexa says she is glad Clarke came and Clarke agrees. That evening, Lexa enters Clarke's quarters and Clarke changes her bandaging. Lexa thanks her. After Clarke is finished, Lexa stands up and bids her goodnight before leaving her room.
In Hakeldama, Clarke and Lexa are returning to Arkadia with the body of the Ice Queen when they encounter the massacred Trikru army. Lexa is horrified and immediately plans to call upon the warriors of the twelve clans to attack Arkadia but Clarke convinces her against it. Clarke convinces Lexa to let her go to Arkadia and try to fix things. Clarke later returns telling Lexa she was unable to convince Bellamy and she instead tells Lexa instead of attack she should have a ceasefire. At first, Lexa is against it before eventually agreeing to "blood must not have blood."
In Bitter Harvest, Lexa is asleep as Clarke sketches her when she awakens from a nightmare. Clarke reassures Lexa that it was just a dream but Lexa assumes it was not just a dream but in fact a warning. Titus enters the room with a crate which he opens to reveal Emerson. Emerson immediately attacks Clarke but the guards pull him off her and Lexa demands he be locked up.
Later, Clarke finds Lexa and Titus discussing the fate of Emerson. Titus believes he should die and Lexa asks for Clarke's opinion. Clarke admits she agrees with Titus if Lexa wants her advice. Lexa then tells Clarke she isn't looking for advice, she's looking for a decision. Clarke enters the throne room to perform the death ritual on Emerson when she stops and instead gives Emerson his life, though he is banished from the lands under the Coalition. Some of the grounders are upset though Lexa calms them by stating that Clarke is leading them to a better future and that the crimes of the Mountain can not be answered by one man.
In Thirteen, Lexa stands with her nightblood novitiates on ascension day when Titus enters the room with Semet who has Octavia prisoner. Lexa is furious that Titus would bring this to her on accession day and asks Clarke for her opinion. Clarke admits she would do anything for her people and Lexa decides to blockade Arkadia, saying that any Skaikru caught across the line would be subject to a kill order. Clarke confronts Lexa about the kill order but she tells her nothing can be done. She then offers for Clarke to stay in Polis as her guest as Titus enters. Titus tells Lexa her feelings for Clarke are putting them both in danger but Lexa declares she is more than capable of separating her feelings from duty.
Clarke is met with Octavia who tells her they'll need to leave Polis soon and she should say her goodbyes. Clarke goes to see Lexa and tells her she is leaving since her people need her. Lexa is understanding and Clarke says that hopefully "someday [they] will owe nothing more to [their] people." They kiss and have sex. After Clarke asks Lexa about the markings on her back and Lexa explains are from her ascension day, each circle representing a life she took at her conclave. Clarke leaves Lexa's room and finds Murphy tied up as Titus points a gun at her. He fires and the bullet misses her, hitting Lexa in the stomach instead. Clarke tries desperately to save Lexa but eventually realizes there is no use. As Lexa is dying, Clarke recites the traveler's blessing and gives her a goodbye kiss. She then watches as Titus removes the flame from Lexa's neck.
Lexa (about Costia): "I lost someone special to me, too. Her name was Costia. She was captured by the Ice Nation whose queen believed she knew my secrets. Because she was mine, they tortured her, killed her, cut off her head."
Lexa: "It's also our only choice, and you know it. You could have warned everyone up 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."
Lexa: "That's what it means to be a leader, Clarke. The truth is, we must look into the eyes of our warriors and say, "Go die for me."
Clarke: "If only it were that easy. Can we please just get back to the plan?"
Lexa: "No. You could be a leader your people look to. Pour their hopes and dreams into. Someone they will fight and die for.
Clarke: "I never asked for that. I'm just trying to keep us alive."
Lexa: "You were born for this, Clarke. Same as me."
Lexa: "And you're willing to risk everything on that? On your feelings?"
Clarke: "Yes. You say having feelings makes me weak. But you're weak for hiding from them. I might be a hypocrite, Lexa, but you're a liar. You felt something for Gustus. You're still haunted by Costia. You want everyone to think you're above it all, but I see right through you."
Lexa: "But you did. You had friends in Mount Weather.
Clarke: "Those deaths were on you, too. The only difference is you have no honor and I had no choice."
Lexa: "You can't run away from who you are, Clarke. Join me, bow before me, and your people will be safe."
Clarke: "Bow before you? You don't give a damn about my people. I know why you're here I made you look weak at Mount Weather, and now the Ice Nation is exploiting that. Well, if you want the power of Wanheda, kill me. Take it. Otherwise, go float yourself because I will never bow to you."
Lexa (to Clarke): "I'm sorry. I never meant to turn you into this."
Lexa and Clarke have both saved each other's lives.
Lexa saved Clarke's life twice. The first time was when she stopped the other Grounders from charging at her and trying to kill her in Spacewalker. The second time was when she attacked Quint to spare Clarke's life in Survival of the Fittest.