At her apartment, Jesse has cleaned up the debris from her fatal battle with Riley, whose body lies on the floor - Jesse zips up the body bag.
Flash to year 2027, where Jesse prepares to leave Serrano Point and Derek, via a nuclear submarine. Derek reveals that he, too, is leaving on a "different" mission, but does not give the location to Jesse. He warns her never to trust the cyborg which is in charge of operating the submarine, telling her to "aim for the chip" in the cyborg if necessary. They part.
In the present, Sarah is packing cash and other valuables to prepare for a move from the house. John offers to sort through their equipment in the garage, where Cameron is packing cyborg spare parts, to John's alarm, fearing Sarah may discover them. He instructs her to bury the parts in the yard, where they can return later to retrieve them, for burning.
After apparently disposing of Riley's body, Jesse hangs out in a bar, and is approached by a Naval officer in a flight suit, who strikes up a conversation with her, noticing her facial injuries. He claims to fly P-3s, a navy antisubmarine aircraft; she refers to "brown shoes," and states she is in submarines, or "bubbleheads," and is programmed to kill robots. He compares the submarine hunting to sheepdogs and wolves; she responds by saying "Sheepdogs hate wolves," and flattens him with a fist to the face. His three Navy friends arise and approach her.
The Connors' neighbor Kaci, no longer pregnant, expresses disbelief that they are moving, and stating that her common-law husband and police officer Trevor is taking care of the baby. A girl was found in the river, shot through the chest - she describes the victim as blonde, with scars on her wrist from a suicide attempt, and a star-shaped tattoo on her wrist. Sarah realizes it is Riley.
John and Cameron continue packing cyborg parts, hiding them just before Sarah enters the garage. Sarah states she needs to talk to John, alone - Cameron steps outside, where she spooks a pigeon, saying "Goodbye, bird, there's a 51% chance I wouldn't have killed you," a reminder of her software flaw that resulted in her killing a bird in "Ourselves Alone." Without audible dialog, Sarah and John talk, then he goes outside, disturbed at the news that Riley is dead. He passes Cameron wordlessly - Cameron tells Sarah she knows, she heard them.
Later, John ominously opens and closes the pocket watch rigged with Cameron's self-termination device. "Was it you? Did you kill her?" he asks Cameron. "I didn't kill her," she replies. He doubts her because she sometimes lies to him, which she admits, but denies that she is lying now. She says she is sorry for his loss - he replies that he wishes he could believe that, too.
Derek and Jesse drive along a dark city street - she is barely communicative, but thanks him for bailing her out, indicating that she became involved in an altercation at the bar, leading to her detention. He presses her about what is going on with her, she says, "nothing." A flash forward to 2027 shows a US submarine in the Pacific, in which the crew is informed by Jesse that they have crossed the equator in a ssw direction, cause for celebration for a crewmember's first time crossing into another hemisphere, for which Jesse reads a proclamation about the event. They refer to a "metal" driving the boat, keeping it on schedule. Suddenly the boat is shaken; the crew believes they are under attack by depth charges.
At ZeiraCorp, Weaver works at her desk, while daughter Savannah, in a playful mood, asks her to play hide-and-seek. Weaver talks about patience and forbearance, and Savannah walks away, finding a door that opens for her, then an elevator door that slides open - she enters, hearing "Three Blind Mice" playing through the elevator speaker. It takes her to Floor Zero, a hallway where Savannah skips along while the wall lighting seems to follow her movements. The lab door opens - John Henry waves her in, asking if she wants to play hide-and-seek. Weaver enters Ellison's office, reporting that Savannah is missing; they begin a search with John Henry, who states that Savannah is hiding, but he will not reveal her location. He requires them to identify an object he is thinking of before he will give a clue to her location. Weaver is willing to play, while Ellison is reluctant to bargain with a computer. Weaver states that they have no choice.
Derek gives Jesse some first aid for the abrasions on her knuckles from the fight, then answers a disturbing phone call. He replies he is on his way, indicating that the caller is Sarah, and tells Jesse that John's girlfriend is dead, the cyborg did it. Jesse tells Derek he cannot kill the cyborg - John must make that decision.
In the submarine, the metal is controlling the helm, while sonar indicates they're being pursued by Metal in the water. The Skynet attack submersible is designated "Kraken," with a displacement of 7800 tons and a speed of 45 knots, a very large vessel. Jesse sees on the scope that they are off-course, demanding that the captain disengage and find a way around the danger; he responds by calling for torpedoes and "one ping" of the sonar to locate the Kraken. A torpedo is in the water; the captain orders a torpedo launch in defense, fuse set to 30 seconds, initiating a dive to 729 meters, the edge of crush depth of the sub. Below the thermocline, the sub will be invisible to sonar. The crew is agitated as they return to their duties, Jesse asking, "What, you've never been twenty centimeters from your Maker before?" She then asks the captain why they are 300 miles off course.
At the Connors, Sarah has found the cache of cyborg parts, including an endoskeleton arm. John enters; he tries to explain they were using the parts for research - Sarah rebuffs him; she was concerned about Riley. Sarah suspects Cameron; John asserts that she did not do it - he knows her, and she told him. Sarah counters with a litany of some of Cameron's lies; John is angered at her and leaves.
Ellison and Weaver continue playing the guessing game with John Henry, while Ellison grows impatient. Weaver counters that John Henry must learn ethics and morals and rules on his own, while exhibiting more facial expressions of enjoyment for John Henry than she does for her human daughter. As they guess correctly, the clues from John Henry finally lead Ellison to a realization of Savannah's location - in the company helicopter on the rooftop.
That night, John goes to the home of Riley's foster parents, meeting the husband, and asking about Riley's whereabouts. He replies only that she did not come home; then the phone rings, he responds as if it is Riley calling. Outside, it is actually Cameron who is the caller - impersonating Riley's voice and claiming to be in Riverside. She asks to talk to John, who takes the phone, talking with Cameron, who finally says, "I love you." John leaves and meets Cameron outside, angry with her about their plan to call the home - Cameron changed the plan by making John part of it and talking to him, adding to the belief by the foster dad that Riley was still alive and forestalling a call to the police. John insists on leaving, alone, and stalks off.
Ellison return to the lab, telling John Henry that he did not have fun playing the game. He lectures the AI on the consequences of it's choice not to reveal Savannah's location - she could have died, it would have been the AI's fault, and it made the wrong decision.
Derek and Jesse return to her apartment - Jesse speculates about John learning what the metal (Cameron) can really do, and maybe some good will come of it. But Derek states that no good can come of it - ever, an innocent kid is dead. They embrace, and enter her apartment. Later, he leaves her again.
In the submarine, Jesse again questions the captain about why they are off course and entering a major Skynet zone. The captain refers to a change in their mission, destination - an underwater oil platform in the Indonesian archipelago, to retrieve a package and deliver it to Serrano Point. The mission orders came from John Connor, but he does not reveal the contents of the package. An armed team is inserted into the platform; they make their way through a labyrinth of steel corridors and doors. The leader spots their objective, disarms, and orders the others to withdraw. He enters a dark chamber alone, raising his arms. Inside are two Ts and one cyborg, with a large case. He calls out, "Connor sent me, John Connor." "I'm just here to pick it up." The cyborg lifts the case.
Sarah begins to burn the cyborg parts as Cameron returns. She tells Cameron she planned to wait for her with Derek's sniper rifle, which would solve about 50% of her problems. She would not have felt bad, but someone would, someone who would never forgive her. Cameron responds that it is about John, his safety, and Sarah is concerned about that. "We're all a threat to John," Cameron says, his worries about family and Cameron making him vulnerable. There is only one way for him to be safe, she says, that is to be alone.
In the city morgue, John finds a compartment listed as "Doe, Jane." Opening it, he finds Riley's body, taking her lifeless hand, which shows signs of a battle. "I'm sorry," he says, rolling the body back in place.
Jesse, in her apartment, sits alone, thinking.