In Red Sun Rising, she is woken up from crosleep by Jordan Green originally to go with Abby's group. However she ends up staying on board the Gagarin with Charmaine Diyoza and Madi Griffin, because Abby didn't want Madi going. She tells Madi that they need to do some training to master the flame.
In The Children of Gabriel, she is sitting on the door of the Gagarin with Madi and Diyoza. She is trying to get Madi to master the flame, but Madi fools around and says that she sees Clarke needing her help. Gaia says that's impossible, because Clarke's mind left the Flame with she left the City of Light. Then Gaia realizes that Madi is not being serious and gives up. Madi the tells her about seeing a commander with scares on his face like lines on a map and wearing all black and that she tries to ignore him. Gaia, shocked, tells Madi that is "Sheidheda" or the Dark Commander and that Madi is right to ignore him. Diyoza the laughs at the two. Gaia stands up and says "Why's it funny?". Dioyza responds it's not, it's sad. Dioyza then quickly stands up pulls out a knife, Gaia thinks Diyoza's going to hurt her and Madi, but she throws the knife into a child of Gabriel. The three are then attacked and paralyzed by parlyptic darts.
In The Gospel of Josephine, Josephine, pretending to be Clarke, enters the room where she meets Madi and shocks the group by suddenly allowing her to go to school. Speaking in Trigedasleng, Gaia questions "Clarke's" sudden change of mind as it risks exposing Madi as a Nightblood. Luckily, Josephine doesn't understand Trig and therefore doesn't figure out Madi is a nightblood.
Later, she help Jordan to find the truth about Primes, they sneak up to the room filled with skeletons where they meet up with Bellamy, Murphy and Josie. Gaia notices that the skeletons have the Flame infinity symbol and wonders if they were all Commanders. Bellamy figures out that the skeletons belong to the original Eligius III Mission Team Alpha. He notices that some of the skeletons belong to kids; and Josie explains that people will do anything to ensure survival for the ones they love. Josie starts urging them to respect Sanctum traditions and leave but Jordan continues exploring. He finds a secret door which leads to a lab.
In the lab, they notice a lot of Becca and Flame-related technology. Bellamy explains that they can't be commanders because Becca didn't invent the Flame until after the first apocalypse. However, she provided her technology to Eligius Corporation before then. Jordan finds a computer and unlocks it using the Eligius III access code. They find a list of video logs. Gaia suggests playing the one titled "Eureka!".
On the video a doctor named Gabriel Santiago is forcibly experimenting on a young woman named Brooke. Josie's old dad is by Gabriel's side, encouraging him. Gabriel explains that they needed to use a fully developed brain and clear the host's consciousness first in order to accommodate the full memory size. He takes out a Mind Drive which looks a lot like the Flame. He knocks Brooke unconscious and inserts the Mind Drive inside her neck. A few moments later, Josie wakes up violently inside Brooke's body. She is proud of Gabriel for reverse-engineering the Mind Drive technology to be able to upload an entire mind into a new host. Gabriel ends the experiment by saying that Josephine was the first success, with more to come.
After watching the video, everyone is horrified by the inhuman experiments they just witnessed. They figure out that the Primes have been manipulating nightbloods to sacrifice themselves to false gods. Jordan calls it murder, but Josie claims the hosts were willing even though Brooke was forced into it. Murphy is indifferent, claiming that back on Earth, he points to Gaia that they used to arm kids to go to war. Realizing that Madi is in danger, Gaia says she will go get her back from school. This helps Josie figure out that Madi has royal blood. She offers to come along.
Later at the bar, Gaia, Bellamy and Jordan are surprised that Clarke seems to be willing to tolerate the Primes' actions. Gaia calls the Primes out for abusing Becca's Flame technology whose intended purpose was to pass wisdom from one person to another. Instead, the Primes want to keep all the wisdom to themselves. Murphy disagrees with her, saying that Becca was just a scientist who was turned into a nightblood in a lab - the same way Abby did to Clarke. This makes Josie realize that it is possible to turn ordinary people into Nightbloods.
In Matryoshka, Gaia works with Echo to get the Sanctum Citizens to rebel against the Primes, blackmailing Ryker Desai into helping them. Gaia eventually allows herself to be captured and is shocked to discover just how much Madi has been possessed by Sheidheda. Raven comes up with the idea to delete Sheidheda from the Flame, but Gaia warns her that Becca's notebook is still in the Machine Shop. After narrowly avoiding being burned at the stake, Raven orders Gaia to get her the notebook so that they can save Madi from Sheidheda.
In Ashes to Ashes, Gaia remains trapped with Nathan Miller and seeks to find a way out to save Madi from Sheidheda or kill Madi if they can't. Miller is eventually able to steal a guard's knife and use a wire on it to pick the lock on a trapdoor so that they can escape. Disguised as Sanctum guards, the two make their way to the Machine Shop to retrieve Becca's notebook. To their shock, Miller and Gaia arrive just in time to save Echo who Ryker is trying to mind wipe. The two explain that they had come for the notebook, not knowing Echo needed their help. Gaia releases Echo who kills Ryker while Gaia is shocked to discover that Echo is now a Nightblood.
In Adjustment Protocol, Gaia hides with Echo and Miller behind the bar in Blythe Ann's tavern when Clarke enters to talk to Priya Desai. Echo realizes that something is wrong and orders the others to attack. To Gaia's shock, it is Clarke and not Josephine Lightbourne. Gaia later insists on joining Clarke as it is her job to protect Madi. Gaia manages to disguise herself as a Sanctum guard, but is recognized by Russell. Clarke convinces the other Primes to take Gaia with them as a hostage rather than throwing her to the Sanctum Citizens who are under the influence of the Red Sun toxin. On Eligius IV, she is held as a hostage by Clarke when Indra opens the door.
In The Blood of Sanctum, Clarke, still posing as [Josephine, threatens to kill Gaia if Indra won't surrender. Though Indra calls Clarke's bluff, stating that they would then have no leverage, Gaia silently signals her mother to comply. In the mess hall, the Sheidheda-possessed Madi orders the crew to attack, leading to several deaths. Once the Primes are gone, Gaia explains to her mother what happened, horrifying Indra who had seen Sheidheda once as a child and knows the evil he can do. Gaia promises to kill Madi if it comes down to it to prevent Sheidheda from being unleashed upon the world.
The group takes Madi to the med bay where Gaia provides Raven with Becca's notebook. With the notebook, Raven is able to hack the Flame, but discovers a kill code installed by Sheidheda that would destroy him at the cost of the Flame. With no other choice, the group agrees to perform the procedure, but are interrupted by Russell who takes Madi with him. Clarke later returns after killing the other Primes, followed shortly after by Russell, Madi and Wonkru. After Clarke threatens suicide, Madi regains control and orders Russell's arrest and Gaia watches on in relief as Madi and Clarke embrace each other. However, Sheidheda tries to kill Madi in revenge. With no other choice, Raven deletes the Flame to save Madi with Gaia holding Madi down during the procedure and looks on sadly as the Flame's code disappears from the computer screen. Eric Jackson surgically removes the Flame from Madi and gives its inert remains to Gaia who bends down next to Madi. When Madi tells Gaia that she's not the Commander anymore, Gaia gives a tearful laugh. However, they are horrified to see Sheidheda uploading himself to an unknown location.