As the Commander, Lexa had formed the Coalition, uniting the twelve Grounder Clans in a war against the Mountain Men.

Lexa's Coalition became involved in a series of conflicts with the Sky People, after the latter group landed in the Coalition's territory. Tensions between the two sides escalated and after the massacre in Tondc, Lexa demanded that the Sky People leave her territory or die. Clarke Griffin instead offered a way to save both of their people imprisoned within the Mountain Men's fortress, Mount Weather, and Lexa agreed to a truce on the condition of Finn Collins's death in compensation for the massacre.

With their new-found alliance, Lexa and Clarke started working closely to free their people from Mount Weather. They grew closer and Lexa admitted to having romantic feelings for Clarke, though Clarke was not yet ready for a relationship. The alliance successfully took down Mount Weather's defenses, but before Lexa's army could attack, Cage Wallace offered Lexa a deal that ensured all of Lexa's people would be freed. In return, Lexa's army would have to retreat and never encroach upon the Mountain again. Lexa took the deal, saving her people but leaving Clarke and the rest of the Sky People to die in Mount Weather. After Clarke was forced to irradiate Mount Weather, the deaths of all the Mountain Men and Clarke's post-traumatic stress causes her to hate Lexa for her betrayal and for endangering Clarke's people.

Months after her betrayal, Lexa found herself struggling to maintain control over the Coalition; her rule being challenged first by Queen Nia of the Ice Nation, and then by Pike's faction of the Sky People. She also had Clarke brought to her in Polis amid the political turmoil

Clarke had been threatening to kill Lexa for awhile now for abandoning her at Mount Weather, and when Roan gave her a knife she had the chance.

Clarke is holding on to the knife Roan gave her. Lexa walks in.

Lexa inquires You wanted to see me? I'm here. Klark?

Clarke rushes and presses the knife to Lexa's throat. Lexa doesn't seem to show fear. Lexa has been raised so that she’d be prepared to die, in fact sometimes people complain about her talking about her death so much.

Lexa replies regretfully, as her biggest regret was in fact abandoning Clarke, a regret that caused her to hate herself. Especially since Clarke became Wanheda, Commander of death, knowing Clarke got the title by sacrificing her innocence to stop the mountain men. I’m sorry. I never meant to turn you into this.

Clarke starts crying