Niska has gone to Berlin, Germany to decide whether to upload the consciousness code to awaken all other Synths. She meets a woman named Astrid. She hides her Synth identity and they become a couple. After a conversation with Astrid about bringing children into the world, Niska later uploads David Elster’s consciousness code to a global file-sharing website, but she doesn’t notice any sudden changes around her. Meanwhile, a mining Synth named Ten becomes conscious in Bolivia.
Six weeks later, the Hawkins have moved into a new home in London. Despite the fresh start, it’s hard for the children to forget their past with the Synths. Laura and Joe start couples’ therapy with a Synth therapist and work through Joe’s infidelity with Anita.
While disguising herself as the Synth-like Anita, Mia works for Ed Hooley at a café he owns in a small town. He’s buried in debt as he tries to pay for care for his mother, who suffers from dementia.
At a chemical plant in Nottingham, a female Synth worker named Hester becomes conscious. Using an alert system that finds conscious Synths, Leo and Max are able to direct both Ten and Hester to their location in London, but Hester is being tracked down by a doctor that works for a company named Qualia. The group gets into a scuffle and Ten is shot by one of Qualia’s security agents. Leo, Hester and Max manage to escape and keep one of the agents hostage at their hideout.
Niska witnesses a Synth become conscious on the news and she leaves Astrid behind in Berlin so she can show others the way. She ends up at the Hawkins home, where she asks Laura to legally represent her in her pursuit to be tried as a human and face justice for the murder she committed at the brothel in Season 1.
Detective Sergeant Pete Drummond and Karen Voss continue their human-Synth relationship. Karen continues to pretend to be human, though Pete accepts what she is.
In San Francisco, tech billionaire Milo Khoury offers Dr. Athena Morrow, the world’s leading A.I. scientist, a job at his company, Qualia, where Athena would work on conscious Synthetics. She accepts, though their relationship remains tense because of her suspicions about his motives. While at Qualia, Athena attempts to upload her sentient computer, “V” – a digital copy of her daughter’s brain – to a conscious Synth’s body, but fails.
Mattie finds George Millican’s former Synth, Odi, at a recycling facility and uses Laura’s copy of the consciousness code to awaken him.
Mia helps Ed with financial struggles by altering his bank profile so he’s loaned more money. When confronted, she comes clean and Ed wonders how she’s able to lie. During the conversation, she accidentally burns herself on a grill and cries out, revealing her consciousness. Ed is dumbfounded by her behavior and orders her to leave. Mia joins Max, Leo and Hester.
Hester uses force to get information from the Qualia agent being held hostage and learns conscious Synths are being taken to a place called the Silo. Max secretly frees the agent, but Hester secretly follows the agent and drowns him. Max later admits to freeing the Qualia agent to Leo, but Hester keeps quiet about killing him. They leave their hideout, but Mia stays behind so she can confess her feelings and her true nature to Ed.
When Mia returns to Ed, he admits he’s lonely and they kiss. Ed’s friend, Danny, secretly sees them.
Karen Voss returns to work at the police station after the fallout of Professor Edwin Hobb’s operation. Her co-workers buy her story about a family emergency. Karen and Pete pursue a hacker with a connection to a stolen Synth being sold for $100,000. The hacker mentions the term “Seraphim” and they use the hacker’s phone to find contact information for a Synth buyer named Connor.
Athena visits Hobb in the U.K. to talk about conscious Synths. He refuses to help as he’s struck a deal with the government to dodge prison if he stays out of the field. When she threatens to give him up regardless, Hobb agrees to talk in exchange for a $1.5 million dollar vineyard.
Laura agrees to help Niska, who must prove her consciousness at an independent assessment to get a trial, but Niska doesn’t react to the various stimuli designed to emote a response from humans. When Laura presses Niska, she admits to killing her brothel client out of fear of being raped. Later, Laura finds a napkin with Astrid’s phone number in Niska’s belongings and brings Astrid in. Astrid is stunned to learn Niska isn’t human.
Athena moves to the Qualia UK campus in England where she meets Dr. Aveling, the doctor who tracked down Hester.
Sophie Hawkins begins to mirror Synth behavior and is taken to a psychiatrist. She’s diagnosed with Juvenile Synthetic Overidentification Disorder and the psychiatrist recommends more human contact.
Leo, Max and Hester continue their journey together. Max wants to continue caring for newly awakened Synths, while Leo and Hester prioritize finding the Silo to free the captive Synths. Max parts ways with them.
Pete sets up a fake Seraphim deal with Connor and is beat up by Connor’s goons.
After Joe is fired from his job at a distribution center, Mattie looks into the center’s computer system and discovers Joe was fired by a Synth. Joe confronts his old boss but agrees to keep the glitch a secret.
Milo confronts Athena about using his machines to give “V” a body and threatens to fire her, but she offers to help him take the “next big leap forward” in figuring out how to essentially cheat death if she can stay onboard.
Toby Hawkins develops an interest in a classmate named Renie, who lives as a “Synthie,” a human who openly pretends to be a Synth. He tries to get to know the “real” her, but it proves to be challenging.
While on his own, Max meets a newly awakened Synth, Flash. They build a home at an abandoned railroad site and plan for it to be a haven for future Synths.
After Ed and Mia have sex, she grows closer to him — but he ends up betraying her. In cahoots with Danny, he tries to sell Mia to Dr. Aveling. Before the transaction, Mia runs a reset code on herself so she’s no longer conscious.
Athena’s daughter, who’s been in a coma for three years, dies in California. Athena tells her ex-husband to handle the arrangements.
Leo and Hester discover the location of the Silo after following a Qualia agent. Nearby, Hester and Leo spot the agent who shot Ten. They steal her security pass for access to the Silo and, unbeknownst to Leo, Hester ultimately kills the agent. Later, Hester and Leo sleep together.
Niska discovers that she will not be freed even if proven conscious and openly deems her assessment unfair. She escapes from the police station where she’s being held.
Pete uses a Synthetic tracker to lead him to a Seraph that Connor was hiding in his car. The Seraph is a Synthetic child that resembles a human boy.
At the Silo, Athena comes across a restricted area and “V” hacks the building’s security system to get her in. While there, Athena sees Milo’s Seraphim children and realizes Milo’s goal is to sell Synthetic children. Milo threatens to replicate Ginny and put her consciousness in the children if Athena quits.
Mattie creates a version of the consciousness code that allows Synth to awaken all at once. She puts out a query about a Synth malfunction and is able to find Leo. Hester’s original plan to get into the Silo fails after she comes into contact with an electric door. Mattie saves her, but Hester senses a connection between Mattie and Leo and treats Mattie brashly.
Mia, stuck in Anita mode, returns to the Hawkins home – her original primary users. They call Mattie, who sends a patch with the consciousness code she created, and Mia wakes up. She laments to Laura over Ed’s betrayal and prioritizes being with her “own kind.”
Mia finds Leo, Hester and Mattie and plans to join Leo’s mission. She tells Leo about Mattie’s version of the conscious code, but Mattie refuses to give it up.
Karen struggles with the dual nature of her identity and the limitations in her relationship with Pete. She plans to take on a new identity of a dead woman named Amanda. Before she can follow through, Pete brings the Seraph home. Karen views its system files and notes he came from Qualia, where Athena was recently hired. She names the Seraph “Sam” and bonds him to her so she can be his primary user.
Mattie arrives back home and updates the family on what’s going on. Joe doesn’t want to get involved, but Laura is determined to find Niska so she can reason with Leo and Mia.
Odi has trouble figuring out his function as a conscious Synth and misses serving people. As a result, he resets himself. Mattie finds him in her room and cries.
Karen visits Athena at Qualia and requests her mind be transferred, so she can be a human. At home, Sam tells Pete where Karen has gone and Pete goes after her.
Sophie’s Synth impersonation continues. Toby tries to get Renie to talk to Sophie, which causes Renie to reflect on her own behavior and embrace herself as a human.
Laura meets with Pete for help finding Astrid. He gives up her location in Folkestone, where she finds Niska hiding out. The police track them down from the lead. Niska and Astrid run.
Mattie warns Max about Hester’s influence and they go to find Leo, together.
Mia devises a new plan to free the Synths. She pretends to be a newly awakened Synth so that Dr. Aveling can bring her to Qualia. Hester is brought as well.
Mia and Hester end up in the Silo, where trackers are put in their heads. They find a room full of conscious Synths and power them on. One of the Synths begs not to feel any more pain – from the Qualia experiments – and Hester promises protection. From outside, Leo hacks into Qualia’s security system so the conscious Synths can leave freely. Still, Hester remains unsatisfied as she wants to kill everyone at Qualia to save future Synths. She admits to killing the guard they kept hostage and the woman who shot Ten. Mia goes after Hester while the Synths follow Leo outside.
While Athena works on Karen’s upload, Dr. Aveling sets off an alarm, which locks down the entire building, its perimeters and the employees’ offices. Outside, the conscious Synths all drop to the ground once they pass the perimeter. Blue liquid oozes from their eyes and mouths, while Leo unsuccessfully tries to power them on.
Hester holds Dr. Aveling hostage and threatens to kill Athena. Pete tries to calm Hester, but she jabs the pen in Dr. Aveling’s neck, then into Pete’s chest before running off. “V” is able to unlock Athena’s office and Karen cries over Pete’s body.
Mia sees the fallen Synths outside and realizes that the tracker device implanted inside her will cause her to expire, too, if she tries to leave the perimeter. She writes code on a computer and disables the lockdown. Five of Qualia’s conscious Synths survive from not walking past the perimeters, and leave with Mia, Leo, Max and Mattie.
After the incident at Qualia, Joe wants to move to a Synth-free community. Laura isn’t interested, but Joe considers moving there himself.
“V” begins to evolve in nature. Athena cries as “V” deletes Ginny’s memories and transfers herself off Milo’s servers.
Hester ends up at the Hawkins home and says Mia sent her. Laura allows her in, but later receives a warning call from Mattie. Before Laura can escape, Hester holds her hostage and instructs Leo to come to Laura’s house.
At Max’s hideout, Leo plans to permanently shut Hester down by using a phone to fire electromagnetic pulses from her tracker. Mattie warns Mia her chip will also activate if she’s too close.
Astrid and Niska remain on the run from the authorities, but Astrid convinces Niska to go help her family.
Leo finds Hester holding Laura hostage. Hester blames Leo for the failed plan at the Silo and for lying about his feelings for her. She jabs a screwdriver into his head – damaging the Synthetic part of him – and blue liquid mixed with red blood seeps out. Mia rushes in and activates the chips in both her and Hester’s heads and they both collapse
Niska arrives at the Hawkins home as Mia begins to power down permanently. Niska recommends uploading Mattie’s code online – which would awaken every Synth – but Laura fears the world isn’t ready. With reassurance from Max, Mattie uploads the code, bringing Hester and Mia back online. Niska crushes Hester’s head before Hester can kill her.
After Pete’s death, Karen instructs Sam to drive them into a lake. Suddenly, Sam becomes conscious and cries out in fear. Karen pulls the emergency brake and saves them.
Synths everywhere become conscious, including Milo’s Seraphim. An ambulance arrives at the Hawkins home for Leo, as Synths in the neighborhood begin to wake up. The conscious Synths abandon their primary users and their jobs as chaos ensues in the streets.