Leaked script plot outline from a few months ago. Spoilers, obviously.
In 2029, the Resistance led by John Connor (Jason Clarke) has successfully destroyed Skynet headquarters. Connor and his best friend, Kyle Reese (Jai Courtney), raid a Skynet outpost in Los Angeles to rescue human prisoners and to investigate Connors' suspicions that Skynet has developed a time-displacement device in a desperate effort to change the outcome of the war by altering the past. They locate the machine and learn that Skynet has just sent a T-800 to 1987 to murder Connor's mother, Sarah Connor (Emilia Clarke), and prevent Connor from being born. Connor then sends Reese to 1987 as well to protect Sarah. Just as Kyle is leaving, Connor is attacked by the T-5000, an advanced prototype Terminator that can turn into a swarm of nanomachines.
In 1987, the T-800 (Arnold Schwarzenegger) begins searching for Sarah when he is confronted by another T-800 (Arnold Schwarzenegger), who destroys the first one with heavy artillery guns.
Meanwhile, Kyle arrives in 1987 and is confronted by two policemen while stealing a vagrant's clothes. The two cops turn out to be a T-1000 (Byung Hun-Lee) and a T-850, who chase Kyle to nearby clothing store. Just as he appears to be cornered, Sarah and the T-800 arrive in a fortified jeep and Sarah exclaims "Come with me if you want to live".
Sarah, Kyle and the T-800 are chased by the T-1000 and the T-850 through the streets of Los Angeles, but manage to hide in a junkyward where they set up a makeshift base of operations, and where Kyle learns that the T-1000 was sent to 1969 to murder Sarah as a young girl, but the reprogrammed T-800 saved her, though her parents were murdered. They've been evading the T-1000 since then, and the T-800 has trained Sarah to be a skilled fighter. She considers him a surrogate father and calls him "Pops", explaining to Kyle.
>"Listen, give Pops a little respect. He studied since their arrival here. He had no clue how to raise children. So he conducted research. Read books. Watched "Sesame Street". Between lectures on how to destroy the cyborg assassins and survive the nuclear holocaust, he took me to museums and zoos."
The trio is located by the T-1000 and the T-850. Kyle destroys the T-850 with a pipe bomb, while Sarah lures the T-1000 into a trap and dissolves him in acid. With the T-800 sent by Skynet destroyed, his microchip is never found by Cyberdyne Systems and used to create the basis for Skynet.
The timeline changes, and Kyle acquires new memories of the future, in which his parents give him an iPhone for his birthday with an advanced Operational System developed by Cyberdyne called "Genisys", which will be uploaded to the Internet in 2017 and become self-aware, becoming Skynet and causing Judgement Day only a few days later.
Sarah, Kyle and Pops decide to travel to 2017 in a makeshift time-displacement device developed by Pops. However, Pops can't travel with them due to the damage the T-1000 inflicted on him, and goes into dormant mode at their junkyard lair, so Sarah and Kyle can find and reactivate him in 2017.
In 2017, Sarah and Kyle reunite with Pops, whose organic exterior has aged, and they set out to infiltrate Cyberdyne Systems and destroy the Genisys Program.
Sarah, Kyle and Pops end up in the hospital, where they are confronted by John Connor. Kyle realizes that the T-5000 nanomachines infected Connor in 2029 after he left for 1987 and brainwashed him into becoming a cyborg loyal to Skynet. Connor then traveled back in time to 2017 to help Miles Dyson (Courtney B. Vance) and his son, Danny Dyson (Dayo Okeniyi), develop the Genisys Program and ensure Skynet's survival and the deaths of Sarah and Kyle.
Sarah, Kyle and Pops evade the police and Connor while attempting to reach Cyberdyne headquarters. They eventually succeed, with Pops sacrificing himself to blow up the facility, destroying the Genisys Program and killing the corrupted Connor. Sarah and Kyle lament Pops' death.
>KYLE: "If a machine could love, he loved you."
>SARAH: "He was not a machine. He was my father".
Suddenly, it turns out Pops has survived the explosion by being coated in liquid metal from the T-1000 assembly line. Now in liquid metal form, Pops reunites with Sarah and Kyle, and they find themselves stranded in 2017, although they have prevented Skynet's birth.
Umbeknowst to them, however, Connor has created a back-up of the Genisys Program, which begins rebooting, and becomes Skynet. To make matters worse, Skynet has begun developing Terminators much earlier to ensure the Resistance is never formed, and is secretly mass-producing an army of T-5000 to destroy the human race.
Cue sequel hook.
