James Ellison dreams of digging out Cromartie's burial site and finding his body. He wakes up, hearing scraping sounds outside his house. He takes a gun from his drawer and goes to the window, seeing a woman outside piercing the yard with a steel rebar. He shines a flashlight at her face, only to reveal it's Cameron. She tells him to go back to bed, and continues piercing the ground.
Sarah and Derek break into an office building, into the premises of a start-up company called Dakara Systems. They confirm that it's the right place, as the scene pans to Dakara's company logo, which is in the distinct triangular pattern of three dots that Sarah saw previously in her dreams in "Complications." Derek asks Sarah why they didn't ask for John's help in this mission, and she replies that she can do this herself, as she rips out the computer's hard drive.
Later at home, John analyzes the files on the hard drives stolen from Dakara Systems. He declares there's only vaporware in them. Sarah asks if there's really nothing in those drives, and John tells her that the files has the design of an AI to handle big problems. The company would have needed a whole server to run it, but right now they have nothing. He explains that it's akin to a terrorist having the plans to build a nuclear bomb, but lacking the plutonium to start up. Derek thinks that it's a dead end and they have been chasing phantoms and smudges that Sarah has found all this while. Sarah believes the company has a connection to whatever they're looking for, citing the facts that they are trying to build an AI, and the company logo of three dots. Derek says that it's just blood fingerprints left by the deceased Resistance member Wells on the basement wall and nothing else. Sarah insists that the dots on the wall meant something.
Cameron returns home and announces to them that Cromartie's body is not buried in Ellison's yard. After a moment of silence, Derek tells John and Sarah that nobody is being asked to stop looking, but the company they are looking at doesn't have the Turk. John thinks that his mother has been looking too hard, but Sarah tells him not to start a debate. He leaves her to ponder over.
The next morning, John tells Sarah that he found information in the drives which state that the company is currently looking for big investors who are willing to contribute start-up money for their new server. He's made her an appointment with Dakara with a cover as a rich divorcee who's interested in putting money on tech start-ups. Sarah asks him if he's spent the night making all these arrangements. John explains that Dakara Systems is a start-up company, just like Cyberdyne once was. Andy Goode's chess program and Barbara Chamberlain's traffic control systems all started small in progress.
Meanwhile, Jesse emerges from her shower to find the surveillance photos she has taken of John, Sarah, Cameron and Derek scattered all over her bed. Derek enters her room with a gun, telling her she has 30 seconds to explain what she has been doing. She thinks he's joking, but Derek maintains his posture and counts down to 25. She explains to him that she was sent back to find John. Derek tells her that she should have told him, but Jesse retorts that Derek should have told her about him living with John and "her", "it", and "metal", referring to Cameron. Jesse says that Cameron has been making questionable decisions which got good people killed. She feels disgusted that Cameron has seemingly taken over the operation. She imagines what John will become if Cameron stays at his side for the next twenty years. Jesse tells Derek she's here to stop Cameron and to save John. Upon hearing Jesse's explanation, Derek takes his gun and leaves, telling her that he will think about it. Jesse asks him what he's doing back here in the past and why John sent him back. Derek shows her a photo of both him and John, telling her that he loves her and not to push it.
Ellison enters Zeira Corp's main entrance with a lot of police and FBI vehicles outside. He meets a former FBI colleague of his, who tells him that a heat wave blew a transformer on Sunday, blacking out half of downtown. A man who was working during the weekend spent eight hours in a sealed room with no air-con and ventilation and got baked to death from the heat. Paramedics wheel out the body, and Ellison removes the sheet. It is Dr. Boyd Sherman.
Later, Catherine Weaver explains to Ellison on Dr. Sherman's job as a consultant on her project here. She tells him that the doctor worked downstairs, in the basement, on the project called Babylon. It is a sophisticated computer program, an artificial intelligence. During the blackout, the AI reserved generator power for itself, but in doing so, shut down the building's other systems. Ellison asks Catherine if the AI has control over the building. Catherine comments that Ellison is making this sound like a monster movie. She explains that the facility and the AI are interconnected only to an extent when the AI needs the facility's resources to help it grow. Ellison questions her if the AI's growth involves the agonizing death of an otherwise healthy man like Dr. Sherman. Catherine says that she doesn't know what the AI's intentions were. Ellison comments that she's now the one making it sound like a monster movie. Catherine tells him that this is what they will find out.
Meanwhile, Sarah and Cameron pose as their covers in Dakara Systems. Upon entering the company premises, they watch two military officers, one of who is a Colonel, taking their leave. Dakara's founder and CEO, Alex Agagi, welcomes Sarah and Cameron to the company. In his office, Alex tells them about the break-in the previous night. He tells them that the robbers took the hard drives and thinks it was industrial espionage. Sarah asks Alex if he's not worried that the company's software design of the AI may be passed off by another as their own. Alex explains that his son Xander builds security measures in all their software, so if someone opens them, they will attack. Cameron asks if this is the reason the Air Force wants it. Alex explains that the Air Force has been interested in AI applications for a long time, as far back as the 80s.
Xander explains that he calls his AI program Emma, after his mother, who died in a car crash in 1984. Alex says that his son barely knew her as he was too young. Alex offers to get coffee for his guests and he and Sarah go out of the office. Alone with Xander, Cameron asks him if he likes chess. Outside, watching his son's interaction with Cameron, Alex tells Sarah that he doesn't pretend to know what is in his son's brain, as he operates differently from what he and Sarah can imagine. Sarah comments that his son needs him, and Alex asks her if she has any kids. Sarah tells her just one, her only son. Alex asks her if her son is challenging, and she tells him it's in a different way. Alex says that parents will do anything for their kids, throw their lives out the window if they have to. Sarah asks what he needs. Alex tells her that last month, he would have needed $100,000 and a little patience, but after the break-in, he would need ten times the amount and a miracle. Sarah asks how much time he's left and he tells her two weeks. Sarah comments that he needs more time than that.
John goes to Riley's house looking for her and meets her foster parents. Upstairs in her bedroom, John tells Riley that her foster parents aren't really what he imagined. She tells John that they are nice, but they are actually immigrants. The rest of the children in the household are not theirs, just losers, cast-offs or rejects as she says. She mentions her foster parents are running a "loser" camp here. The two change topics, talking about the posters Riley owns. John looks at a poster of a bear eating a fish, but Riley presents a more cynical view, saying that the poster is about the fish and not the bear. John is stunned by her thoughts, and decides to leave, but Riley tells him to stay. She asks him if he came here for a reason.
Sitting down, John tells Riley that he promised to explain everything to her, back in Mexico. He thinks that he has nothing to explain about the truth, nothing he can say. Riley tells him that he doesn't need to say anything and it's okay. She tells her she would like it if he just sits around with her, but John apologizes to her and leaves.
At home, Sarah presents a more credible link of the three dots to Cameron, an AI with a name and a strong sense of self-preservation, plus relations with the United States Air Force. Sarah asks her what does all this information add up to her. Cameron replies simply that it's not the Turk. From her conversations with Alex's son Xander, she says that he doesn't play chess but prefers Go, which the Chinese invented 5000 years ago. She takes out a Go board and two bowls of black and white markers onto the table. She tells Sarah that Xander said it's been calculated that there's more possible Go games than there are atoms in the universe. He offered to teach Cameron how to play the game. Sarah asks if he offered to tell her about the AI, but Cameron replies that it's not the Turk as Xander doesn't play chess. Sarah thinks this may be pieces to a puzzle which they have seen before. Cameron tells Sarah about "strange things happen at the one two point," a Go proverb which means that the usual rules don't apply. Sarah insists it's always the same rules and they always apply. Cameron says that Dakara has no money and will miss the Air Force's deadline. Sarah tells Cameron to get the money for the company and give it a miracle. Cameron asks how she knew and Sarah tells her that this was written in blood on the basement wall, showing her 3 white markers in the pattern of the dots on her palm.
Riley goes shopping at a dress shop, until Jesse arrives, asking her if she wanted to talk. It is obvious they knew each other. Later in the dressing room, Jesse caresses Riley's hair, commenting that she looks tired. She asks her if she slept enough. Riley reveals to Jesse that John came to visit her today. She thought that he was going to tell her everything. She thinks that what's John was meaning to do but nothing happened as he just left. She feels that there's something wrong and off-balance, but Jesse thinks John's reaching out to her. Riley tells Jesse that John ran away from her, but Jesse shakes this off as he's still a boy. Riley goes up to the mirrors and asks Jesse if she noticed that there are a lot of mirrors in this world. She tells Jesse that she doesn't think she can do this anymore. Jesse apologizes and says she understands it's not easy, and maybe Riley may have some feelings for John, as he's the reason why people follow him out of hell. Riley asks what if she wants out. Jesse asks how she would do that, as there's nowhere to go. She tells Riley there's no out. She kisses Riley's head, telling her that she can and have to do this.
John and Derek approach their house with more supplies from Derek's store. Derek shows John a belt with three dots and asks if he's seen it. John, who's annoyed, tells his uncle that he understands that he wants to talk about his mother when she's not even here. Derek says that he sees the three dots not only on the belt, but everywhere else. He thinks that it's crazy to start seeing things in every corner and on every wall and pretty soon, will even forget what they are looking for in the first place. John says that he always remembers what he's looking for. Derek asks him if he's sure. John questions Derek angrily on his judgment. Derek tells John that he wants to make sure that he's seeing clearly. John doesn't reply and leaves.
Sarah and Alex go for tea break in the city. They talk about their sons and his wife. Alex tells Sarah about the chess tournament the Air Force sponsored a couple of months ago. A friend of a friend of his who works for the company that sponsored the winners reveals that they have a prototype chip of 12nm, which is small enough to fit onto the end of a finger. They quietly put it through its paces and if a real world test works, they would all be very rich geniuses. Sarah asks what he and his people need. Alex wants a deposit of half a million dollars from her to show her seriousness in investing. Sarah asks Alex if he thinks the chip works. Alex tells her that it's the future.
Ellison visits Zeira Corp's basement with the lead programmer of Babylon, Matt Murch. He notices that the server rooms are all kept at freezing temperatures, and Matt explains it's to keep the server towers from frying. Ellison talks briefly with Matt on the subject of the name Babylon, the legendary city that was destroyed by God. Matt thinks that God gave the project a shot yesterday, as the blackout should have shut down the AI completely. He explains to Ellison that Babylon routed all the power from the generators to keep itself running. Ellison thinks the AI broke the rules but Matt believes that it invented new ones. He asks Matt on the job Dr. Sherman does with the AI, and asks Matt how it feels about the doctor. Matt thinks it's ridiculous as a computer won't be able to feel about a human. Matt thinks it's impossible that the AI knew that it was killing Sherman when it threw the switch, from what Ellison concludes, but hopes it isn't so.
Meanwhile, Sarah and Cameron throw together all the diamonds and money they have to find that it's not enough for the investment deposit. Cameron says that they will need everything to be enough and Sarah agrees on this idea. Cameron asks her if she's certain and Sarah tells her that certain is a luxury. She sees a pattern of three dots made by diamonds when she keeps them, as Cameron reminds her that usual rules don't apply.
Later that night, Sarah and Cameron gather with Alex and his people at a high-restaurant. Alex learns that Sarah is using cash to pay her deposit and she tells him that she doesn't like banks. They make a toast and Cameron gives a speech in Japanese, impressing the Japanese representative Hideo Minamoto. Later, Xander theorizes to Cameron about how souls and consciousness may be able to be downloaded onto chips and run it, as she only smiles in return. Xander asks her if she's going to eat anything as she has not touched her food. Sarah asks Minamoto when he will hand over the chip they need. He passes them a small box and Xander examines the chip, confirming that it's real. He passes the money over to Minamoto as the representative leaves, telling them it was a pleasure doing business with them.
Riley goes home to her foster family, as her foster mother tells her that she missed dinner again and to get it from the fridge. As she prepares her food, Riley hears her foster brother and sister arguing over possession of the TV remote. Frustrated by the normal life, Riley tells off her mother, brother and sister that they are all crazy as they sit in their cozy house and do their usual stuff as if it all matters. She tells them this lifeisn't real and will burn until they're nothing but bleached skulls. She tells them they are all dead. Her foster mother tries to calm her down but Riley pushes her violently away. She is shocked by what she did and apologizes and leaves the room.
Back at Dakara Systems, Alex thanks Sarah and Cameron for their help as Xander is excited at analyzing the chip. Watching them both outside the office, Sarah tells Cameron how they would be burning their dreams to the ground. Xander loads the chip's program on his laptop, but is stunned to see a processor error in the CPU's memory. Alex thinks it's a hiccup, but Xander keeps getting the same results. Cameron offers to look at the chip and tells them that its is actually 40nm, not 12nm. The chip was motor-designed to give a more advanced appearance, which means they have been duped.
Later, Alex tells Sarah about his family's old dry goods store, which was taken over by neighbors after they cheated his grandfather to sign a pact which allows them to watch over his store for him. After the Japanese were rounded up after Pearl Harbor, the neighbors condemned his grandfather's property and deeded it to themselves. Sarah tells Alex that he couldn't have known about Minamoto, but he tells her that he will fix the problem and make it right and pay her back every dollar, no matter how long it takes. Sarah tells him that this is not important right now and offers to talk to Minamoto. Alex tells her that she doesn't talk to someone like him, as Minamoto is from the Yakuza. Sarah receives a message from her cell phone, telling her that target is acquired and moving to location.
Meanwhile, Ellison tells Catherine that all they know are the facts, the means and opportunity except intent. Catherine wonders why he asked Matt Murch about all this and not directly ask the Babylon AI itself. She tells Ellison to ask "John Henry," which is what Dr. Sherman named the AI. Later in the basement, Matt explains to Ellison that the AI communicates through images and recognizes voices, and tells him to talk to it. Ellison talks to the AI and introduces himself, as it pulls up an image of him and his credentials on the screen. He asks "John Henry" if it knew Dr. Sherman and the AI confirms it, through binary code "1" and a picture of Sherman. Ellison asks it if it worked with Sherman yesterday and the AI confirms it. He asks it if it worked with the doctor today but it denies it. Ellison asks why and it shows an equation which means 'no operation".
Ellison tells the AI to show him what happened to Dr. Sherman. It then shows a security video of the doctor working inside the lab at the basement. Catherine explains to Ellison that the doctor was the lab when the blackout occurred but the emergency generators went online. Power went to the server room instead. Dr. Sherman tried to leave but the electronic door failed. Security and bio-metric monitoring went offline. Ellison tells the AI to show him security video and bio-metric at the time the external power returned. The video shows Sherman's body slumped near the door. Catherine tells Ellison that Sherman's heart had stopped and his body temperature was almost double the standard ambient temperature, well above human survivability level, which means he was dead. Ellison notices that the AI displayed a message saying that "Medical Attention Required". He asks the AI if the doctor was alive at that time and it says no. He asks it if it thought the paramedics could help if it called them and it says yes. He then asks it if he, Ellison, is alive and it says yes. When he asks it if he's dead, it shows the "no operation" equation again. Matt says that the AI doesn't understand the question. When Ellison asks the AI how it feels about Dr. Sherman, it again shows the "no operation" equation. He asks it if it knew that it caused the doctor's death when it redirected power to the server farms, and it says yes. Ellison asks the AI what image it associates with that information but it is unable to produce any. Ellison concludes that the AI has no feeling for what it did. He tells Matt that he taught the AI procedures and rules, but never about moral and ethics. He says that whether the AI had any feeling over Sherman's death doesn't matter, so long as Matt teaches it to value Sherman's life, which he didn't. Ellison tells Matt and Catherine that someone killed a man and it wasn't "John Henry," the AI, and leaves. Catherine asks after him what he would teach it if he could, and Ellison replies that he would teach it the Commandments, starting with the first ten.
Sarah, Cameron and Derek break into Minamoto's hideout. Sarah punches Minamoto and then steps on his hand with her high heels, making him scream in pain. He tells her that he doesn't have the money and is just a hired actor. Sarah asks him if it's the real Minamoto or the Yakuza that hired him. She demands to have the real chip. He tells her that the chip was handed to him by Alex as a ruse. Sarah thinks that Minamoto's lying, almost preparing to shoot, but Derek tells her that he's not lying. The three of them leave, with Sarah kicking Minamoto, telling him that he never saw her face.
John meets the trio outside, asking how it went. Derek says that everything is simple, Minamoto was an actor and they now know who hired him. Sarah insists the three dots, the Air Force and the chip mean something. Derek tells her all those details were nothing and whatever she needed it to be, that's what it is. He says simply that she just got played and it happens.
Back at Dakara Systems, Alex calls out for his son, to find no response. He reaches the company entrance only to get beaten up by Sarah. Throwing him against the wall, she asks Alex who he's working for. Alex claims not to know what she means but Sarah tells him not to lie as she hates liars. He tells her that he's not working for anybody, just him and Xander, as Sarah throws him onto the ground and punches him in the face. She tells him that she would have blown up his office sky high if she was still in the nuthouse. Alex apologizes profusely about her money, but Sarah tells him it's not about the money and continues beating him. Alex asks for his son but Sarah demands to know about the chip, the AI and the three dots. Not answering her question, Alex begs Sarah not to hurt his son. Sarah tells him that he always talks about his wife, his poor grandfather and now he talks about his son. Alex retorts that he did it for his son and the three dots were just a logo, as Sarah punches him a final time. She then drags him to see his son.
At the office, Sarah pulls Alex to a chair where Xander is being held by Cameron. Sarah forces Alex at gunpoint to tell the truth about himself to his son. He reveals to his son that there was no chip and he made it all up just to cheat Sarah of her money. He hired Minamoto and his men to do the dirty work for him. He tells Xander that they will never be able to make the deadline with the Air Force as there's no chance. As Xander listens in shock, his father tells him that he had to make sure he was taken care of. Xander tells his father that his design of the AI can work, but Alex tells him that he hopes he's right, but he sometimes barely understand what he's saying. Now he wonders if Xander will understand him. Alex tells Sarah and Cameron that their money is in his desk and to take it and go. Both go, leaving father and son to stare at each other in silence.
Jesse returns home to find Derek sitting at her bed. She jokingly regrets giving him her keys. Walking over to her, Derek reveals to Jesse that John is his nephew, telling her that she's the fourth person to know that fact. Jesse looks unfazed, while Derek tells her that he came here to fight a war, to do whatever it takes to stop Skynet. If they're going to do this, he feels there's no more room for secrets. He says if there are any secrets she hasn't told him, he needs to hear it now. She tells him that when they were stationed at Serrano Point back in the future, she had been using his toothbrush the whole time. Derek tells her that he wasn't using it to brush his teeth, and Jesse smiles. They embrace, but Jesse has a certain look in her eyes.
John waits for his mother to come home and then embraces her. There is knocking on the door, and John tells her that it's Riley looking for him. Sarah tells him she will be okay. At the front door, Riley tells John that she's rejecting his rejection of her. She asks him if he wants to go for a walk, and John tells his mother that he's heading out with Riley. Getting no reply, he goes out.
As Sarah cleans herself up in the bathroom she notices in the mirror bloodstains from Alex that form the three dot pattern on her cheek. She abruptly destroys the mirror.
Catherine tells Ellison that she has thought of what he said the night before, about rules and the Ten Commandments. She feels that she's not qualified to teach John Henry all those things. She doesn't know how, so that's why Dr. Sherman was here. She tells Ellison that she wants to show him something. Taking the elevator to the basement, Catherine tells him about John Henry, the mythical man from folklore who raced a steam-powered hammer through the mountain, one man alone who challenged the machine, only armed with an iron hammer. Ellison knows that he won, but his heart gave out and he collapsed and died. Catherine tells Ellison that John Henry defeated the machine, but he couldn't stop progress.
Steeping out of the elevator, Catherine opens the door to the lab, leading Ellison to see something shocking. Cromartie's body, apparently alive and repaired, sits in a chair, connected to the servers.
"Hello, Mr. Ellison," the robot says as it lifts up its head, "My name…is John Henry." It smiles. Simultaneously, the AI communication screen displays, "How are you today?"