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During the Operation Chrono, Skynet's complex in Colorado was destroyed. When the Resistance members were parting Kyle Reese, Skynet attacked and transformed John Connor into a T-3000 Terminator before it killed other Resistance members present. However, this action led to the creation of an alternate timeline.
- See also: Genisys
In this new timeline, John came to Cyberdyne Systems and provided his technology know-how to help Daniel Dyson and his father, Miles Dyson, to restore the Skynet Project under a new project known as "Genisys", a program able to integrate and connect the private, public, and military network. John also used his future knowledge to create a massive vat of unprogramed mimetic polyalloy for use once Skynet came online and to start building the Time Displacement Equipment though by 2017, only the quantum field generator was in place.
After learning of this due to his memories of the new timeline, Kyle Reese and Sarah Connor traveled forward in time to 2017 to stop the full activation of Genisys, knowing that it would be unstoppable at that point and Judgment Day would begin. Aiding them in their efforts was Guardian, an aging T-800 that had been sent back to 1973 by an unknown party to protect Sarah from an assassination attempt but had to stay behind in 1984 because of its damage on living tissue outer sheath.
Guardian had a hand in the construction of Cyberdyne building that housed Genisys by acquiring a job as a construction worker between 1984 and 2017 before he was laid off. As a result, he was also able to learn the weakness of the building. Hampered by John, Kyle, Sarah and Guardian set out to destroy Genisys before it could come online. In order to stop them, John pushed up its activation from thirteen hours to fifteen minutes. The three planted explosives, but John destroyed the detonator while Skynet, growing closer and closer to activation, taunted them through holograms. Finally, Guardian destroyed John in the prototype Time Displacement Equipment's magnetic field and it set off the explosives, destroying Cyberdyne Building and apparently Genisys. While the three had succeeded in stopping Judgment Day, Skynet's system core, which was located underground, survived the explosion. Skynet became self-aware, though its plan was delayed.
- Skynet in Terminator Genisys timeline has demonstrated more emotions than its other previous counterpart. For example Skynet disdains John Connor's victory and taunted him. In addition, Skynet refers its minions as "slaves" and show its superiority over them.