When Crono's party arrives in the Prehistory era, Ayla saves them from Reptites and brings them to Ioka. That night, they have a party. Crono and his friends first meet Kino here, who questions why Ayla would have a party for someone who is not from Ioka. When the party awakes, they find that all their equipment has been stolen, so they tell Ayla, who goes with them to find out what happened. They visit the Forest Maze where Kino is, who tells them that he had taken the party's equipment because he was jealous of the attention Ayla was giving Crono. Ayla hits him for this and tells him that she likes Kino more, so he apologizes to Crono and Ayla. Ayla tells him to give them their equipment back, but he tells them the Reptites had stolen the equipment from him. Ayla tells him she will continue with Crono's party and tells Kino to go back to Ioka and protect the village. After getting their equipment back from the Reptites, the party comes back to Ayla's hut, where Kino tells them he wants to be stronger than Crono.
After being transported at the Fiendlord's Keep by a Gate, the party awakes in the Prehistory in a hut, where Ayla tells them she found them atop Mystic Mountains. She tells them to rest as there are badly hurt, and the next time they wake up Kino enters their hut and tells them that Ayla is busy trying to find the village Laruba. Another villager then enters, telling Kino that the forest to the north is on fire, who runs to the burning woods. When the party arrives in the forest, they find the ruins of Laruba and are told by a villager that Reptites had kidnapped Kino. Ayla and the party head to the Tyranno Lair and find and rescue Kino, who also wants to join them. Ayla tells him that if she dies, then he has to be the chief of Ioka. Upset at hearing this, Ayla assures him she is strong and that she will not die. Kino says he knows and wants to show them something. They follow him to the entrance where he opens a large skull that leads further into the lair. He then tells them they are strong and that he was weak and jealous, and then leaves.
Later, when the party has defeated Azala and Black Tyranno at the lair, Lavos starts to enter the earth's atmosphere, heading right for the lair. Kino suddenly appears along with Dactyls and saves the party. Ayla offers to help Azala, though she refuses, saying that Lavos is "the will of the earth". Ayla tells her she will not forget her, and Azala tells Ayla to take care of the earth. As Kino and the party fly off on the Dactyls, Lavos crashes into the Tyranno Lair and destroys it, leaving only a large crater.
When the party defeats Lavos, he and Ayla appear at the Moonlight Parade. Marle tells him that he is her distant ancestor and that he better have strong, healthy children, to which he replies, "No worry. Ayla MUCH energy!" Marle asks what he meant by that, at which Ayla says, "Kino dumb! Ayla go now!" and pushes Kino into a Gate, blows a kiss to Marle, Lucca, and Crono, and then enters the Gate herself.
In the PlayStation, Nintendo DS and Steam versions of Chrono Trigger, a cutscene shows Ayla seemingly skipping proposing to Kino opting instead to put a ring on his finger right away, showing that they were married after Ayla returned to the Prehistory after defeating Lavos.