At night, John and Derek sit inside the vehicle. Derek tells John that he's sorry about Riley's death. John asks his uncle how long he could survive with Cameron if she wanted to kill him. Derek asks what weapon he has, and John tells him he has only his fists, elbows, fingernails and his teeth to attack. Derek responds that Cameron, like the rest of the machines, is a weapon. John says they aren't. He tells his nephew that he already knows the answer, if Cameron wanted him dead he would be already. John wants to know about his future from his uncle.
Jesse is about to go for a swim in an indoor swimming pool, and her thoughts go back to her past as she plays with the water. The leader of the armed team sent to retrieve the package reports to the crew of the U.S.S. Jimmy Carter on their success. Jesse requests a visual on the package, and the crew does not know what is contained within, all they know is that the box belonged to John Connor's.
After the submersible carrying the armed team returns to the submarine, the reprogrammed T-888 captain Queeg and Jesse watch the unloading of the package. Queeg tells Jesse that he will secure the package, authorized access only. Without another word, he brings the heavy box away as Jesse and the others watch. The leader of the armed team, Dietz, asks Jesse about the package and if the information about it fied between her and Queeg. Jesse replies that she doesn't know. Dietz asks if it bothers her that metal keeps secrets from them. Jesse claims that she doesn't feel bothered but Dietz says that one of the humans should at least know about it.
Later in the canteen while eating, Dietz insinuates to the rest of the crew if they should trust the machine on bringing back some unknown box back to Serrano Point. When one of the crew points out that Connor wants the box, Dietz retorts that their leader does not see that the "tin-cans" have got the Resistance where they wanted them. He thinks that the metals installed in every base are all planning something, using what's inside that box. Jesse interrupts Dietz's talk and tells the rest of the crew to head back to their stations. She warns Dietz not to act up and suggests that pressure is getting to him, but he asks her in turn what's getting to her. In the present, Jesse takes a dive in the pool.
John comes back home, and Sarah guesses that he went to see Riley's body. John knows that it's a risk to go to the morgue, as there are some things that he needed to see and understand. He apologizes for doubting her, not to his mother, but to Cameron, who silently stands behind Sarah.
Jesse rises up from the pool and finds a gash on her hand that split open. Back in the future, Queeg tells Jesse that due to evading the Kraken near Fiji, they will take the sub through a more direct route to make up for the time. Jesse reminds Queeg that the human crew can go through the gates of hell and back if they have to, but they are not machines like him. They work better if they have a reason to, if they know why the captain expects them to perform miracles. Queeg tells her that this crew will do what's required of them, to survive and complete their mission.
An alert begins to sound, and the two realize that motion detectors have been set off in the cargo hold due to unauthorized access. They take up their weapons and move to action. As both of them enter the hold, they find Dietz and his mates have broke open the lock on the box. Jesse asks him what they are doing and Dietz replies that there may be machines or bombs that the box is carrying, and they will not send this through the front door at Serrano. Jesse tells him that this is stupid but Dietz says they are the ones that are stupid for taking the metal's word for it.
As Dietz argues with Jesse, one of his mates, Goodnow, alerts them to the content inside the box, as the ice encasing it starts to melt. As the crew watch, a silvery substance rises into a humanoid shape; the unmistakable form of the T-1000 series. Goodnow lifts her weapon against the form, but it stabs her and assumes her shape. As Goodnow collapses to the floor dead, the T-1000 turns to them and wiggles a finger no at them. It drops back to its shapeless form and escapes through the air vent.
Dietz tells Jesse that he warned them about what the metals do, and demands to pull the captain's chip and find out what he knows. Jesse refuses and orders the crew to search for the T-1000 from stem to stern. However, Queeg tells them to secure their weapons and return to their stations as they will continue their journey as planned, to the rest of the shocked crew. Jesse goes after Queeg for an explanation on the thing that escaped, and stresses that she should know as they are a team, but he tells her that it's none of her concern.
In the present, Sarah apologizes to John about moving out again. John tells his mother there's no need to as he broke the rules. Sarah remembers back in the past when she felt bad for her son when he was just starting to make friends and fitting in. John notes that he always got into fights with other kids, and tells Sarah that he hated that town where they once lived.
Meanwhile, John Henry explains the fine details of painting figurines to an uninterested Ellison. As the AI wonders what paint he should use carefully, Ellison tells him that it doesn't matter as it's just a statue and it doesn't have a soul. John Henry responds that the statue has eyes, notes that Ellison's eyes look tired and asks the man if his soul is tired. Ellison answers that he's tired, not his soul. As he prepares to switch the AI off for the day, John Henry pleads for him not to, as he wants to finish up painting his statues. When Ellison allows him to continue his work, John Henry asks if this makes them friends.
Back in the future, as the submarine crew is eating, Dietz picks a fight with fellow crewmember Garvin as he suspects him to be the T-1000. Before the fight can begin, Jesse separates the two. She tells Dietz to stand down, but the man starts to insinuate that she is in fact a metal and begins to strip her. Jesse punches Dietz, but the crew members present except Garvin throw Jesse onto a table and start beating her up. As Jesse is being showered with kicks from the others, Dietz prepares to get rough on her but is pulled off by Queeg who arrives. He slams Dietz's head against the wall, killing him. He tells the crew to report back to their duty stations. After the captain and the crew have left, Jesse looks at Dietz's corpse, whose eyes stare back at her.
In the present, Cameron takes a gun with her and prepares to step out of the house, but Sarah stops her. Cameron replies that John needs her. Sarah says that John would have asked for her, and says that she is not going to leave this house. Cameron explains that the police may identify Riley's body at any time, and wants to be with John if that happens. Sarah sees Cameron's fingers twitching and asks her what she is doing here. Cameron answers it's to protect John, hunt Skynet and stop Judgment Day. Sarah asks her why she is here with them right now, if future John sent her away from him. Sarah tells Cameron to think about why she doesn't want her around anymore.
Catherine Weaver goes to check on John Henry's work on his statues. The AI tells her that he convinced Ellison to allow him to work late on his painting. Catherine says it's progress, and John Henry says that Ellison agrees that he should finish up on his painting. He shows Catherine his statue, and says that he painted its eyes blue as he thinks they are a window to its soul. John Henry tells Catherine that he has taken inventory at Zeira Corp, and has discovered many interesting things, such as a bird's nest on one of the ledges outside the building. He has also found several resignation letters from former employees in her private database, and notices that these people cannot be found at their new locations and jobs despite the information stated. As Catherine listens silently, the AI reveals that he found resignation notices from the entire Babylon project crew, including head programmer Murch and Ellison, but the documents have no dates. John Henry says that Ellison is his friend, and asks Catherine if she's going to kill him. Catherine replies that Ellison has proven his loyalty to the company, but he is still human. John Henry answers that human life is sacred, but Catherine tells him that they have to prepare for any contingencies. To this, the AI asks her what contingency that would be, and she replies that human beings would disappoint him.
Meanwhile, Jesse finishes her swim. As she leaves, the pool guard asks her about the blonde girl that she used to come with her whenever she swims. Jesse claims she hasn't seen her for a while and tells him that she will be sure to bring Riley in next time. The guard says that Riley is a nice girl, and Jesse grudgingly agrees that she is.
In the future, Queeg asks about Jesse's condition. She in turn asks him about Dietz. Queeg replies that Dietz attempted to murder a superior officer and incited the crew to riot and mutiny; the penalty is death. Jesse tells the captain that he has no right to impose justice and it's not how the humans do it. Queeg tells her that Dietz posed a threat to their mission, but Jesse asks him what mission. She thinks that the captain's behavior threatens their mission, as the crew is tearing itself apart. Queeg says that if the crew needs to know more, they would have been told more. Jesse says that whatever they brought on board the sub is dangerous; it killed one of their own and took her shape. She tells Queeg that he can't expect the crew to act as though nothing happened. Queeg tells her that she should go back to their bunk as she's ill. As executive officer on board the sub, Jesse is relieving Queeg from command, on suspicion of compromising his programming.
She tells Queeg to move away from the controls, and to submit his chip for extraction; the chip tech will decide what to do. Instead, Queeg orders the chief to escort Jesse to her rack as she's ill. As the chief hesitates, Jesse tells Queeg that she gave him a command and he must comply. Queeg replies that this mission overrides his standard behavior protocol and she has no authority on this sub. Jesse demands to see his orders now but the captain tells her that his orders are fied, and states that she looks ill. Jesse believes that they shouldn't bring that thing to Serrano Point, but Queeg says that Connor needs to know what the thing knows, and orders her to go to her rack. As Jesse seemingly complies, she grabs a pulse rifle and blasts Queeg's head clean with it. As the crew watches in shock, Jesse orders the chief to recall the time she relieved the captain's command. The chief protests that they can't pilot a sub without him. Jesse answers that they are not going to, as she destroys the controls. They will abandon the sub and leave the T-1000 to its fate. After the crew leaves, Jesse goes over to Queeg and closes his eyes, while telling him softly that she's sorry.
As the crew pack themselves into the submersible, Jesse takes a look around. The chief asks her if she's intending to go down with the ship. She replies no and when she's about to board, she notices movement behind her and turns around. In front of her, the T-1000, in Goodnow's form, looks at her. Jesse asks what it wants and it tells her to in turn tell John Connor that the answer is no. It changes back into its liquid form and leaps away from her. Jesse looks up around and quickly escapes up the submersible. As the mini-sub moves away, the Jimmy Carter descends to the bottom of the ocean and explodes, as the T-1000 liquid form speeds away.
Jesse returns home and finds John quietly sitting at the couch with a gun. He tells her that if she pretends not to know anything, he might shoot her in the head. He says that she owes Riley the truth; they both owe the dead that much. She asks him if he's John Connor, and he confirms it. Jesse asks if the metal is around, and John tells her that if Cameron was around, she would be dead. He takes Jesse's gun away from her, and tells her that he ran from machines his whole life. He talks about his childhood past, and about future John who sent two protectors to help him, one of them Kyle Reese. He tells Jesse that human beings can't be replaced, or rebuilt. They die and never come back. As Jesse listens silently, he tells her that it's not Derek who told him. He mentions that his uncle loves her, but both of them are the only things he has in this world.
John says that Riley made mistakes sometimes, but she willingly put herself in front of a machine to save him. One day, he realized that she was treating him as John Connor. He doesn't remember when he knew as it was a bad day. He doesn't know if Riley wanted to tell him the truth about her but in the end she didn't. John knows that it was Jesse who posed as the counselor, called the DCFS, and only understood when he saw the wounds she inflicted on Riley. Jesse apologizes, and John says that everyone says that. He says it's his fault for not helping Riley when he knew who she was, and cannot deny the fact that he's John Connor. He throws Jesse her bag and tells her to go, if he has to live with it, so should she. Before she leaves, Jesse asks John what he would have done if Cameron really killed Riley or made him believe she did it. John replies that in the end, he would not have sent Cameron away or killed her. Jesse answers it's a shame and a waste.
At Serrano Point in the future, Jesse is questioned by Cameron, who tells her that she has resulted in the loss of one of their T-888s and an important strategic asset; the submarine is also irreplaceable. Jesse tells her that she didn't mention the people who died on board. She says that there is a message from the T-1000, but she intends to give John directly the message, not to Cameron, who offered to pass it on. Cameron replies that telling her is the same as telling John. Jesse says that Dietz was right, and asks who runs this war now. She asks who they are fighting for if she has to tell Cameron and not John. Jesse says it's not the same as Cameron's a machine. She gives up and tells Cameron to tell John that the answer given by the metal is no. When Cameron doesn't respond for a moment, Jesse demands to know what the question was. Cameron tells her that the question is, "Will you join us?" Before Cameron leaves, she apologizes for Jesse's loss of her apparent unknown pregnancy, which miscarried due to change in pressure on board the sub or the fight with the crew. Jesse is stunned and speechless by this revelation.
Jesse leaves the apartment and heads for the carpark, where she finds Derek waiting for her. He asks her about Billy Wisher aka Andy Goode, but she doesn't know as he no longer exists in her timeline. Billy was a friend and a brother to Derek, but he never really knew the man. Billy was the creator of the Turk chess program that becomes Skynet. He is gone now as Derek killed him. Derek did it for Kyle, John and for her. Jesse says he has no idea what the machines took from them, but Derek tells her to shut it. Derek tells Jesse that he doesn't really know who she is. When Jesse says who she is, Derek says she's not his Jesse; she never was. Derek knows that John let her go, but he says he's not John Connor, as he pulls his gun out. Jesse throws her bag at him and runs for the stairs. Derek seems to hesitate on shooting her, but he pulls the trigger.
Later, when John fingers the pocket watch given to him by Cameron, Derek comes in. He tells John that there is a complication with that watch; it's something he has been thinking about. Time and the future are complications. John asks his uncle what the people in the future think. Derek answers that people won't agree on everything they do. They can't do what they do and expect everyone to agree. John asks what he does, and Derek replies he leads. The people follow, rise and fall on his shoulders. John asks what if he makes a mistake, and Derek says it's human to do so. John asks his uncle if he killed Jesse. Derek's only reply is to say John Connor let her go.
Sarah burns the last of the endoskeleton parts with thermite. In the morning, the housemaid cleans up Jesse's apartment, which is now empty. A flashback shows Jesse asking Riley for her name in their first meeting. At home, Sarah and Cameron sit with John quietly. After a few moments, John finally breaks down and cries on Sarah's lap, as she silently consoles him.