In Red Sun Rising, She was part of the mission team on Alpha. She was there when Russell Lightbourne went psychotic.
236 years later, she along with her family steals the Gagarin to escape the eclipse in Eligius IV. She and the others throw knockout gas canisters to knockout Skaikru and Niylah. After Charmaine Diyoza kills her brother Daniel and father Victor, and Madi kills her mother Faye, she explains that they were trying to avoid the eclipse, later revealed to be a lie.
She reluctantly agrees to take Abigail Griffin, Octavia Blake, Raven Reyes and Jordan Green to Sanctum. On the ground, she sees a grave on the opposite side of the radiation shield. When she asks them "Who's Shaw?", Raven breaks up in tears. She disables the radiation shield, though she hesitates at first, allowing Abby's group to go to Shaw's resting place. She lets them inside Sanctum's radiation shield. After the group makes their way into Sanctum, some children climb up the stairs after the eclipse and see the group. Kaylee says she's ok to a pre-teen girl named Rose, even though she has handcuffs on.
In The Children of Gabriel, she was present when all of the adults returned to Sanctum after the Red Sun. She later entered the room where, Clarke Griffin, Abigail Griffin, Bellamy Blake, Octavia Blake, Raven Reyes, John Murphy, Echo, Jordan Green, Nathan Miller, Eric Jackson and Emori are being held with her fellow Primes, Russell and Simone Lightbourne. She tells Russell that Clarke was not there and identifies Raven as the pilot. She then gets hasty when Russell mentions retrieving the transport ship. He tells her that she will be going with them, and Kaylee acts scared. He says "Now you're afraid to leave the shield?" She explains to him that they were late to seek shelter and took the transport to seek shelter. She later goes with Bellamy, Octavia, Echo and some guards to retrieve the ship, when they near the site of the ship, they hear the Children of Gabriel chanting and Kaylee tries to go to her family but the guards tell her no and escort her back toward the village. Octavia tells Kaylee not worry.
In The Face Behind the Glass, she attends the naming ceremony of Delilah Workman. She stands between Russell Lightbourne VII and Miranda Mason as he mentions the Four Pillars of Sanctum, Repent, Renew, Rejoyce and Rebirth, he apologizes to Kaylee for leaving her and her family behind during the Red Sun. They hug.
In The Gospel of Josephine, she is called into the dining room in the Palace to see Russell and Simone. They both question her about how she and her family were trying to run away from Sanctum, when they took the Gagarin. She claims she doesn't know what they're talking about when Josephine walks out and Russell and Simone tell Kaylee that she told them. Kaylee questions them, why they'd believe a stranger, thinking Josephine is Clarke Griffin. Josephine calls her "LeeLee" and reveals that they were at one time best friends. Kaylee is shocked. Then Josephine reveals that six years prior Kaylee pushed Josephine's previous host out the window and killed her. As Kaylee tries to reveal that Josephine killed her lover named Isaac, Josephine stabs Kaylee with a dinner knife in the neck. She falls to the floor and the host dies.
In Memento Mori, Josephine pressures her mother into deleting Kaylee's and her family's minds from their mind drives.
In Nevermind, when Clarke and Monty Green enter Josephine's mindspace Clarke discovers that Josephine's memories are books. Clarke touches one. It reveals a flashback to the day Josephine VII's body died. Kaylee and Josephine VII sitting in Josephine's room chatting while Josephine paints a picture of her original body. After this, Kaylee reveals that she drugged Josephine and demands why she killed her lover, Isaac. Josephine reveals that Isaac was a threat and he defied the will of the Primes. However, Kaylee defended Isaac's action, claiming that he defied Oblation and he would never hurt anyone. Kaylee and Josephine have a fight and Kaylee pushes Josephine out the window to her death.
In Adjustment Protocol, Russell introduces Emori as the new Kaylee and Murphy as the new Daniel to explain their presence amongst the Primes and why the two haven't been resurrected. After noticing Murphy and Emori holding hands, Gabriel Santiago informs them that Daniel and Kaylee were siblings, causing them to quickly let go of each other's hands.
In The Blood of Sanctum, Murphy and Emori continue their ruse as Daniel and Kaylee for the sake of the Sanctum citizens in order to save their friends. However, Kaylee's objections to the Adjustment Protocol force Murphy to help Gabriel save the people in the tavern instead of Emori. Gabriel tells the two that Kaylee's objection to the Protocol was what allowed the Adjustors to buy their act when Murphy and Emori saved their friends.