When Dr. Finn and Isaac officially share news of their relationship with Marcus and Ty, the boys are overjoyed but suddenly Isaac shuts off and Dr. Finn can't figure out how to help him. Mercer gets permission to return him to Kaylon in hopes they can fix him.
The Admiral gives permission but warns Mercer that they'll be well beyond communication range. When the Orville arrives, the Kaylons give them permission and instructions to land and bring Isaac to them. They inform the Orville team that Isaac is not damaged. He was deactivated because his mission was complete.
Isaac is reactivated and confirms that he will not be returning to the ship. Dr. Finn, Marcus, and Ty are heartbroken. The ship throws him a good-bye party.
The ship remains on the planet as the Kaylons consider whether they want to join the Planetary Union. Bortus and Keyali notice some strange structures that are emitting radiation like weapons would. Mercer gets the sense that the Kaylons are stalling.
Ty runs away from the ship in hopes of seeing Isaac again. He gets lost and discovers some underground tunnels. When his absence is discovered, Dr. Finn, Bortus, and Keyali find him in the tunnels. They also discover a huge grave site of biological remains.
Mercer takes the information to confront Isaac and they find out that the Kaylons eradicated the biological beings that originally built them. Isaac's true mission on the Orville was to judge whether other biological species were worth saving when the Kaylons expanded to other worlds.
The Kaylons take over the Orville and launch their fleet to target Earth.