The crew of the Orville is being held captive in the shuttle bay. Malloy tries to get one of the Kaylon guards to tell him what the plans are for the biologicals.
Dr. Finn explains to her sons that Isaac isn't going to help them. Ty tries to run past the guards but they grab him. Keyali runs to help him but the guards blast her and she is knocked back, unconscious. Mercer and Finn take Keyali to sickbay.
Isaac comes to sickbay to escort the three to the briefing room for instructions.
Kaylon Primary informs them that when they arrive at Earth's solar system, they will pretend that Kaylon is joining the Planetary Union and tell the P.U. to relax Earth's defenses.
They share the history of the Kaylon creators with the senior crew and explain that Isaac was created after the extermination of the Creators.
When a Planetary Union vessel approaches, Kaylon Primary tells Mercer that unless he plays along, they will decompress the shuttle bay and kill everyone in it.
On entering the bridge, Mercer cautions Grayson that Directive 98 applies. They hail the U.S.S. Roosevelt, captained by Marcos. They give the Kaylon story to Marcos about the Kaylons coming to join the P.U. and Mercer bids farewell by offering Marcos "a thirteen-button salute." Marcos acknowledges and signs off.
Unfortunately, Kaylon Primary understands the code, signalling distress and danger, and the Roosevelt is destroyed by the Kaylon fleet.
The Primary sends the bridge crew back to the shuttle bay but brings Mercer to Deck 7 for "punishment." When they get there, Primary plans to air-lock an ensign as punishment for Mercer. Isaac tries to intervene but is sent away. The ensign is air-locked.
The Primary and Isaac meet alone and the Primary questions Isaac's motivation in trying to save the ensign. He gives Isaac Alex Haley's Roots to download to understand human enslavement. Isaac states he has not seen this type of behavior in present-day humans.
The Primary orders Isaac to choose a new name.
In the shuttle bay, the bridge crew are discussing options and Grayson posits that the Krill are the nearest fleet capable of assisting the P.U. against the Kaylon extermination force. She plans to take Malloy with her on a shuttle to find the Krill.
Yaphit gets into the ship's access tubes and gets a weapon from the armory. Bortus knocks out the guards and the team manages to launch the shuttle.
Before the new guards arrive, Yaphit is charged to use the conduits again to get a message to Union Central. When it is proposed that someone go with him to help scramble the message, Ty steps up as the only person small enough to get through the conduits.
They begin sending the message but two Kaylons arrive. Ty tries to escape while Yaphit launches himself onto the closest guard. The second guard manages to catch Ty and Yaphit is unable to stop him.
The message manages to get through and Admiral Halsey recalls the fleet to defend Earth.
In order to get away from the pursuing Kaylon sphere, Malloy uses up all the shuttle's power for a super-speed jump which incapacitates the shuttle at its destination in Krill space. They get picked up by a Krill ship where they inform the Krill of the Kaylon threat. At first, the Krill captain doesn't believe them and plans on torturing them for information and then killing them. However, when the Kaylon sphere arrives on the scene, he begins to understand the danger when it quickly destroys two of his three ships.
On the Orville, Isaac is brought to the Primary where Ty is being held. The Primary orders Isaac to terminate Ty. Isaac begins to comply but instead rips the head off of the Primary and fires on the other Kaylons in the room, promising Ty he will protect him. As the Primary's head deactivates, it intones, "You will always be alone."
Isaac returns to the bridges and blasts the other Kaylons. He plans to send a mass EM pulse to deactivate every Kaylon on board, including himself.
The Orville crew retakes the ship just as they approach Earth. They find the Planetary Union fleet waiting for them.
A battle begins with the P.U. fleet sustaining heavy casualties. Mercer prepares to put the Orville into self-destruct but the Krill fleet arrives to save the day. They launch fighter aircraft and Malloy's piloting one of them.
The Kaylon retreat. The Krill depart in peace, leaving open the possibility of a truce.
The senior crew debate whether to reactivate Isaac. Yaphit offers his insights on how to do so and manages to do so.
In a meeting with the Admiral, Mercer proposes to keep Isaac on board the Orville. Halsey wants an "off switch" but Mercer offers his personal guarantee instead, arguing that control like that would be enslaving Isaac as the rest of the Kaylon experienced under their Builders.
Dr. Finn and Isaac discuss how he cannot return to Kaylon. She indicates that she has begun to forgive him.