We did get vague hints about this, and there were also rumors about John Connor (Jason Clarke) being the anatgonist in Terminator: Genisys, and the new trailer for the movie confirms the fact.
The clip starts with Sarah Connor (Emilia Clarke) talking to John as a young boy, asking him to leave and never look back. The visuals then capture a ravaged earth after the nuclear holocaust, then the camera cuts to Clarke as John, with his heavily scarred face. "My whole life I prepared my son to lead humanity in the fight against the machines, but there is one thing I couldn't prepare him for," Sarah Connor's voiceover plays in the backdrop. The story is familiar up until now, as there talk of the game being rigged and the Terminator being sent back in time to kill John's mother, with Kyle Reese (Jai Courtney) volunterring to go back in time and rescue her.
When Reese lands on earth, Sarah picks him up and informs him that she and the Guardian (Arnold Schwarzenegger) have been prepping for his arrival over the past decade. But then comes the big twist, when Sarah meets John in the present, all grown up, and before we know it, the Guardian, Sarah's protector attacks John, revealing that he is a T-1000.
On March 26, Screen Rant posted an interview with Clarke from a visit to the set of Genisys from last year. In the interview, Clarke revealed how there was potential for John Connor to pulverised in Genisys, and he would be quite vulnerable, stating that, "There's room for him to be really destroyed, knocked about."
Earlier this year, the leaked script for the film had also revealed that John would play villain in this instalment.
Terminator Genisys is scheduled to release in July 2015.
Watch the trailer: