At a coastal cemetery, a long line of graves marked only with "1984," stretches into the distance. Sarah stands near the entrance, gazing at the markers. Derek joins her; she states, "I don't know which one is his" - referring to Kyle Reese, her long-ago lover. Derek refers accusingly of her arrangement to meet him and Cameron in the desert, but she instead went to the Lighthouse. "We stopped to see Charlie," she explains, and he is dead - Derek learned that from a call from John, who then joins them. Derek believed that his brother Kyle, buried there, counted for something in a relationship with Sarah - but to her, John counts more, and Derek keeps too many secrets.
John offers a question which is not a question - "Well, everybody dies from here, right? On a cell phone he found at the Lighthouse after the battle, a photo of little Savannah has been found. John had seen her at Dr. Sherman's office - she was a patient there, but Dr. Sherman is dead. John leads the group from the cemetery to pursue this lead.
At an elementary school, Savannah is among the students learning new words through a computer display, but she is secretly exchanging messages with John Henry, who replies, "Words are fun. I know 228,312." The teacher detects this breach of instructions, and sees the exchange, to which Savannah responds, "I'm just chatting." Later, Weaver meets the teacher, who is concerned that Savannah may be in danger from her unknown friend, John Henry. In the playground, Weaver asks Savannah about her contact with John Henry - she was teaching it words to a song. Assuring her that John Henry would not hurt her, she instructs Savannah to avoid discussing it.
At the ZeiraCorp lab, John Henry regards himself in a translucent screen - Ellison is there questioning him. John Henry wonders about brothers - and if Ellison's looks like him. John Henry's "brother" is a computer, Ellison explains, but JH was referring to datasets - are they the same? Do they share the same thoughts? But Ellison says John Henry is unique. The human brain, John Henry says, has great capability, but it is flawed - nowhere to download it's memories when you die. The Bible solves this dilemma by introducing the concept of heaven, which to John Henry is "billions of souls, no bodies." It's possible heaven has a hardware problem, since so much of it is required to process just one entity. John Henry needs to know what his brother is thinking, what it plans to do. "I don't want to die again," a statement indicating that the AI is self-aware, and is determined to survive.
The Weaver residence is a stark glass-and-steel building. Savannah does homework; she is in the company of a young woman. Savannah answers her cell phone - the caller is John Henry, but she says she cannot talk. As he tells her to use the headset, a van arrives, and a uniformed man approaches to deliver a jug of drinking water. Suddenly the monitors in the lab display security video from the residence - John Henry watches the man and Savannah. The sitter answers the door - the smiling man pulls a pistol and shoots her dead - it is a Terminator. John Henry gives Savannah instructions to hide. A security service calls, indicating the breach has been detected - a response team is underway. The T searches the house as JH watches, and sends Savannah to the garage. Her headset shows the T she is out of range - he moves toward the garage. Savannah runs in fear to the car - suddenly she is in the arms of John.
The T finds them, shooting rapidly. Sarah enters, firing several rounds into the T's back; it turns, as Cameron pushes Sarah aside to absorb several shots. Derek finds the dead Debbie, while Cameron begins battling the T, allowing Sarah, John and Savannah to run, while John Henry watches the fight unfold. The T disables Cameron, and pursues the others. Cameron reboots, and follows. Derek moves to the T, pistol drawn, but it shoots Derek down. Outside, it finds the others, but Cameron intercedes, throwing the T down the hillside. Inside, they find Derek dead - Sarah takes his cell and weapon - "Keep moving," she tells John. John Henry watches them escape.
Ellison enters ZeiraCorp, finding Det. Craig of the LAPD with Weaver. Craig reports the attack on the Weaver residence, which resulted in the deaths of four security guards and one gunman, who was Derek, and Savannah is missing. The other deaths are unexplained. Heavy security is in effect as they wait for kidnapper demands and identification of Derek. Weaver sends Ellison to add names of Savannah's friends - he knows to query JH in the lab. Craig knows Ellison's history, but Ellison has little information. As Ellison enters the lab, John Henry's first question is "Why did you stop looking for Sarah Connor?" Then JH shows the security video of Sarah - Ellison admits he is not surprised that she is alive. Sarah did not kill the guards, JH confirms, it was the T, on the monitor for Ellison to see. Ellison does not want anyone to know this yet, not even Weaver - JH must keep this secret. JH asks is Sarah will hurt him, since she blew up Cyberdyne and killed Miles Dyson. JH views Cameron on-screen - asking "Who is she? She is like me..."
Sarah, John, Cameron and Savannah hide at a garage, mourning Derek. Ellison calls Sarah - he got her number from JH. Sarah will not return Savannah yet, but agrees to meet Ellison downtown. When he arrives in his Mercedes, Cameron enters, the plan changed. He lied to her before, she says, and she should have killed him then. "Drive!" Sarah and Ellison meet - she took Savannah to protect her from the T; Ellison admits only that he works for ZeiraCorp, still not revealing that he was responsible for returning Cromartie from Mexico for further experiments by Weaver. She tells him Derek and Charlie are dead. She wants to talk to Weaver; he wants Savannah.
Weaver wants JH to show her the security videos - he claims a faulty sector on a drive. Ellison and Weaver leave the lab to talk. Meanwhile, John talks to Savannah, who remembers him from the counseling sessions with Dr. Sherman. Savannah is sorry about John losing his friend. She talks about John Henry, her friend who lives in the basement. John asks more - and she explains JH has a cord in the back of his head, and he cannot leave the basement. Mr. Ellison talks to JH, she says - he teaches JH "stuff."
Ellison explains to Weaver that Sarah took Savannah to protect her from a machine, and that he hid the videos from her. She insists on staying to protect JH; Ellison does not understand why Savannah is not uppermost in her mind. But Savannah's survival may someday depend on JH. She instructs him to arrange a meeting with Sarah. Det. Craig informs Ellison that the gunman, Derek, was an escaped felon, but was not killed by the security team's weapons, and Ellison had investigated Derek earlier. Ellison understands why he is under suspicion, and leaves the heavily-guarded corporate building.
John now brings to Sarah what he has learned from Savannah about John Henry, plugged into a computer. He shows a photo of Cromartie's human predecessor - apparently having shown it to Savannah for identification. Sarah had destroyed the chip (in Cromartie), but John believes John Henry is not Cromartie, some something bigger, worse. Cameron says Ellison should be killed; Sarah insists on no more killing. Ellison calls; Sarah agrees to return Savannah, and meet with Weaver soon after.
Craig questions Weaver about Ellison, and his arrest for murder, but Weaver responds that he was cleared. Weaver confronts JH about his lie at the behest of Ellison, and he asks her what would happen if anyone learned that she is not Savannah's mother, not anyone's mother. If he told Ellison, she says, that would be unfortunate...for Ellison. Regarding Savannah, JH relates that Ellison taught him that human life is sacred, but Weaver suggests that word has the same root as "sacrifice." JH refers to the story of Cain and Abel - "Which brother am I?" Perhaps in this story, Weaver responds, "You are God."
John virtually apologizes to Cameron for failing to meet them in the desert. Sarah had her reasons, Cameron says. He will miss Derek. Future-John also knows what it is to lose people he loves, she explains, and Sarah planned to leave John with Charlie. John knew about her illness, but thought her lump was only the transmitter - Cameron responds that Sarah has lost weight. Sarah enters, they must leave with Savannah.
John sits with Savannah in a dark theatre, Cameron and Sarah waiting for a rendezvous with Ellison. If the meeting with Weaver is aborted, Sarah vows to leave the ZeiraCorp in ashes. Ellison arrives, assuring Sarah he is alone and will be in touch about a meeting with Weaver, then takes Savannah. Sarah walks out of the theatre, finding herself at gunpoint by numerous police. John and Cameron follow, but when she sees they are undetected, she assaults the police to create a diversion. Inside, John is enraged at Ellison, who says, "John, I swear I didn't know." John vows to kill him, then escapes with Cameron. Outside, Sarah is subdued and handcuffed, watched by the T, present in the crowd. In a voiceover, John Henry begins singing the Scottish folk song, "Donald, Where's Your Trousers?" as Savannah is returned to Weaver. Sarah is led away while a news broadcast bills her as an escaped fugitive, and John and Cameron watch on a storefront screen. In the lab, John Henry and Savannah sing the song together, as a small box of ashes - Derek - is buried in the coastal cemetery, unidentified, marked only as "2009."