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. As Lexa worked to bring peace to the clans, Clarke forgave her and they became allies again and later lovers. Lexa's Flamekeeper, Titus, disapproved of their relationship and during an attempt to kill Clarke, shot Lexa by accident instead. Despite Clarke's desperate attempts to save her, Lexa died from her wound.

As with all of the Commanders before her, Lexa's consciousness continued to live on in the Flame upon her physical death. When Clarke took the Flame to destroy A.L.I.E. in the City of Light, her mind summoned Lexa's consciousness to aid her.

Lexa hugged Clarke tightly Clarke, I’ve missed you!