Kaeon was captured by the Terran Dominion, and renamed "subject #383" as part of Project Blackstone. Dr. Jake Ramsey refrained from calling him by his designation, with Dr. Martine disagreeing with him saying that the protoss were not his friends, and that they'd tear the place apart if they weren't locked down in the psi-dampening chambers.
Kaeon and the other protoss being captives, became more responsive after Dr. Held was transferred to one of the facility's sub-levels, Kaeon being less resistant to the test than the others. By the time Dr. Held betrayed the staff, he was the last living test subject. When Held turned on the base's staff by releasing zerglings into the upper levels, Dr. Talise Cogan found her way to the lower levels and released Kaeon. He then killed Dr. Held "merging" with his brain. Kaeon was found by other terran survivors.
When Dominion forces arrived to rescue the survivors, Valerian Mengsk offered the survivors a place in the Brin. Kaeon was offered transport to wherever he wanted, but Kaeon had become fascinated by Ramsey's condition (as per his experiences with the preserver Zamara) and was willing to advise the group on xenological matters if he in turn were allowed to examine Ramsey's sensitivity to the protoss' forms of communication. Ramsey and Kaeon spent a great deal of time conversing and apparently reached a mutual understanding.