Kyle Reese (Jai Courtney) remembers what his parents told him of the world before Judgment Day. He never got to witness it, but he heard it was beautiful. On August 29th, 1997, Skynet took over and unleashed Judgment Day upon the world. Massive explosions are seen hitting San Francisco, killing millions of people and destroying the city.
As a child, Kyle is running through the sewers to avoid the Terminators. One of them corners him in the darkness, until it is shot down by the Resistance leader John Connor (Jason Clarke). He takes Kyle with him, and Kyle grows up fighting alongside John as they try to stop Skynet once and for all.
In 2029, John and Kyle fight with their unit to infiltrate the last Skynet base to take their secret weapon - the time machine that sent the Terminator to the past to kill John's mother Sarah Connor (Emilia Clarke). Although Kyle isn't immediately convinced the mission will work, John persuades him to continue fighting alongside him. He then gives Kyle a picture of Sarah.
John gives a rousing speech to the other Resistance fighters before Kyle infiltrates the Skynet base using a dead Terminator to enter. The other Terminators scan it and see it's non-functional, so they start shooting at Kyle's truck. He detonates several explosives, killing these Terminators and allowing the other fighters to attack. Skynet's flying machines attack, shooting down some fighters in the battle. Suddenly, all the machines go offline and fall. The fighters think they've won. They go down to the storage facility to find the time machine. John tells the fighters what happens with the Terminators and his mother, and he asks for a volunteer to go back and stop them, because if Sarah dies, then he is never born, and all their victories will be undone. The original T-800 (Arnold Schwarzenegger) is already sent back to 1984 Los Angeles to carry out the task. Many offer to go back in time, but Kyle ultimately steps forward and decides to go since he knows as much about Sarah as John based on what he's told her. John agrees, and Kyle steps into the machine. As he is being sent back in time, Kyle sees one Resistance fighter, Alex (Matt Smith), with his arm glowing as he grabs John. He whispers, "You didn't think it was going to be that easy, did you?" to John. Kyle calls out to John as he is sent back.
In the time jump, Kyle sees flashbacks of a childhood he never lived, before Judgment Day. He sees himself on his 13th birthday receiving a tablet for Genisys, an operating system that is set to go online soon in this timeline. The young Kyle looks in the mirror and repeats "Genisys is Skynet", and that it's ready to activate in 2017. He also sees himself with Sarah, who traces her finger in the palm of his hand saying, "A straight line. You keep moving forward and never look back."
The T-800 approaches the trio of punks to take their clothes. Before anything else can happen, an aged T-800 (which Sarah has nicknamed "Pops") arrives and shoots at the original T-800. The two Terminators fight and pound each other's skin off. From a distance, Sarah uses a sniper rifle to shoot the original through the chest, killing it.
Kyle arrives in 1984, nude. He takes the pants off a homeless man as a cop (Byung-hun Lee) pulls up by the alley where Kyle landed and chases after him. Kyle quickly learns that this man is also a Terminator, the shapeshifting T-1000. Kyle runs into a clothing store and grabs a shirt. Two actual cops find him and cuff him. The T-1000 kills the older cop while Kyle and the younger cop hide. When it looks like the T-1000 has them cornered, a truck plows into the store and smacks the T-1000. Sarah opens the door and yells to Kyle, "Come with me if you want to live!" Kyle does so and hops in the truck with her.
Sarah apparently already knows who Kyle is and what he was sent back in time to do. She tells him they already killed the Terminator sent back to kill her, and she knows about Skynet, Judgment Day, and her own son. Kyle is surprised to see Sarah's Terminator (Pops) is working with her. In a panic, Kyle tries to shoot him, but Pops knocks Kyle out. While he's unconscious, Pops and Sarah discuss how she already knows that she's supposed to fall in love with Kyle and conceive John, but she doesn't want to hear about it. Meanwhile, the T-1000 follows them using a piece of his liquid metal to track them. The T-1000 catches up with them and attacks. Kyle comes to and shoots at the T-1000's police cruiser, causing it to blow up.
The trio lead the T-1000 into the sewers. Using its liquid metal, he reactivates the dead T-800, which attacks Kyle. Kyle manages to knock its head off, destroying it for good. Sarah finds herself in a floor beneath multiple vats of acid. Kyle runs to her, saying he's hurt, until another Kyle runs by. Knowing one of them is the T-1000, Sarah tries to figure out who is the imposter. She shoots at the T-1000's foot, which bleeds the liquid metal. Sarah tells the real Kyle to run as she shoots the acid vats to hit the T-1000. He nearly catches up to Sarah until Pops grabs him and holds him beneath the acid until he is completely disintegrated.
Sarah tells Kyle how Pops was sent to her in 1973 when she was a child and he vowed that nobody would hurt her. She and Pops bring Kyle to a place where they have their own time machine. Sarah wants to jump back to 1997 to prevent Judgment Day, but Kyle remembers the flashbacks he saw and is convinced that they need to jump to 2017 when Genisys is set to go live. Sarah is unconvinced until Kyle tells her what he saw. Pops knows what he's talking about and says he went through a nexus point that created an alternate timeline, which happened the moment Kyle reached out for John when he saw him being attacked in 2029. Sarah finally agrees to go back to 2017. She and Kyle undress for the machine as they talk about Kyle's time with John. Pops stays behind since his arm was damaged by the acid and he needs time for the tissue to repair, so he will spend the next 33 years waiting for Sarah and Kyle to return.
The two arrive in 2017 in the middle of a highway. They are nearly hit by a car until Kyle grabs Sarah and gets slammed against the front of the car. They are apprehended by Detective Cheung and Lt. Matias (Sandrine Holt and Michael Gladis). Pops (now more aged with grey hair) sees them.
Sarah and Kyle are taken to the hospital. There, they are met by a man named O'Brien (J.K. Simmons), who happens to be the cop that survived the T-1000 attack back in 1984. He knows there's something unusual about Sarah and Kyle. Sarah notices one of the doctors with a Genisys countdown on his phone and asks about it. She and Kyle learn that Genisys is an operating system set to link up with every electronic device in the world, meaning it's basically Skynet in the making. Matias also mentions to them that after running their prints, it looks like Sarah is the only one that is off the grid, but Kyle's prints match the Kyle Reese in this timeline, who is 12 years old. The authorities leave when Homeland Security arrives. Moments later, Sarah and Kyle are met by John. He has them cuff two officers when they enter the room. He convinces Sarah that he is her son when he mentions that she would sing him "Rocket Man" as a child, but he jokes that her singing is awful.
The three go to the parking garage where John calls Kyle "Dad", leading John and Sarah to admit what Kyle never knew, that he is to be John Connor's father. Kyle is confused and upset until they're met by Pops holding a giant teddy bear. He's concealing a gun, which he uses to shoot John. Kyle then thinks that Pops really is a murderous Terminator, until the blood around John turns into mechanical particles. John explains that when he was attacked in 2029, he was turned into a Terminator, the T-3000, by Alex. He convinced John that the reason they couldn't prevent Judgment Day was because of him, and he is better off as an asset to Skynet than he is as their enemy. He tries to convince his parents to join him, but they refuse. John attacks, and Pops fights him. They crash into the hospital and tumble near an MRI machine. The magnetic pull holds John back long enough for the three to escape.
We see a brief interview with Danny Dyson (Dayo Okeniyi), son of Miles (Courtney B. Vance). Danny is the President of Cyberdyne and creator of Genisys, and he hopes for the program to be a success.
Pops takes Sarah and Kyle to a safe house near the Golden Gate Bridge where they prepare their weapons to fight back. Kyle is still upset over learning he is John's father, having been lied to by both him and Sarah. She also tells Kyle that he is fated to die if everything goes out the way it should. Eventually, they resolve to destroy the Genisys mainframe for good.
John is apparently working alongside the Dysons as they prepare to launch Genisys. Danny speaks before a large crowd and shows off a childlike avatar in the role of Genisys, saying it is eager to meet the consumers. Danny says they have reached a billion pre-orders. Meanwhile, John vows to not let anyone harm Genisys.
Sarah, Kyle, and Pops get ready to fight back when John finds their hideout. Sarah shoots John with an explosive, giving the three a chance to run outside. They take a school bus before John re-emerges and chases after them on a motorcycle as they ride over the Golden Gate Bridge. John latches onto the bus and pulls the brakes out, causing Sarah to lose control. Kyle and Pops try to hold John off until he causes the bus to flip over and slide over the edge of the bridge. Pops pulls Sarah and Kyle out while John falls into the water with the bus. The authorities arrive, and the three surrender since Pops doesn't have a good chance of taking out all the cops.
The three are taken into custody. During their interrogations, O'Brien brings in the 12-year-old Kyle with his parents. Neither of them recognize the adult Kyle, but young Kyle says the adult looks like his father. They leave. Pops notices through the two-way mirror that something is up with one of the detectives. Cheung appears to shoot the other detectives, and Pops breaks through the mirror, knowing she is John in disguise. O'Brien helps Sarah and Kyle escape. Sarah then finds 12YO Kyle still with his parents. She traces his hand with her finger and tells him to keep going and never look back. O'Brien guides Sarah and Kyle to the roof with Pops where they take a chopper to Cyberdyne. John takes a chopper of his own and follows.
In the air, Sarah shoots at John, but he keeps going. They get high above John's chopper, giving Pops an idea. He looks at Sarah and says, "I'll be back" before dive-bombing into John's chopper and causing it to crash.
Everyone makes it to Cyberdyne, with John having made it first. He kills the guards and jumps the Genisys countdown from 13 hours to 15 minutes. Sarah, Kyle, and Pops plant explosives around the facility as they head to find John. Sarah and Kyle encounter the Genisys avatar and shoot out the projectors as it continues to taunt them. They, along with Pops, fight against John as he tries to prevent them from doing any further damage to the facility. Pops gets the detonator to set off the explosives, but it's too close to Sarah as John has her in his grasp. Neither one can kill her, since Pops is still protecting Sarah, and John needs her for him to stay alive. Pops fights John while Sarah and Kyle encounter Genisys in a matured avatar form, taking on the appearance of Alex. He says he cured John and that there's no stopping Skynet from becoming a reality.
Pops takes the fight with John to the room where an unfinished time machine is located. John's human tissue gets blasted off, revealing his complete T-3000 form. He continues to fight Pops, doing severe damage to him. Pops impales the T-3000 with his arm and brings him into the now-active time machine. He traps both of them in the magnetic field and tells Kyle to protect Sarah. Kyle gets her out of there as the magnetic field gains more power. Pops gets pushed out of the time machine and falls into a pool of mimetic polyalloy liquid while the T-3000 is destroyed in the magnetic field. The explosives go off and blow up most of the facility as Sarah and Kyle get into a bunker before the explosion hits them. After a while, Pops comes back, having been "upgraded" in the liquid metal.
The three go to find 12YO Kyle for Adult Kyle to tell his younger self to keep repeating "Genisys is Skynet". Now free from the threat of Skynet, Sarah is happy to choose what happens in her future, and she chooses Kyle, pulling him in for a kiss while Pops looks on awkwardly. The three drive off, with Kyle saying that even though Skynet is gone, there are still questions left unanswered, but they will continue to move forward.
Midway through the credits, we go through the ruins of Cyberdyne, where we see that the Genisys core is still active. The holographic avatar shows up and looks up at the core.
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