He told the New York Post that events will "unfurl in a very unexpected way for the characters and the audience".
"With as much humility as I can muster, I will tell you that I feel like this season start in a really strong place and it continues to delight us," he said. "Some of the stories coming up are really fun and exciting."
He added that viewers will "absolutely" see the Doomsday Machine that is linked to Peter (Joshua Jackson) be activated before the season's end.
"To me, surprise is a good means of storytelling, but sometimes giving the audience what they expect in an unexpected way is more satisfying," he explained. "As an audience member, I love guessing ahead on stories I care about. That's how our minds indicate they're really engaged."
Pinkner also confirmed that the Fringe production team are still planning ahead for future seasons, despite concerns about the show's ratings.
"We have six to eight seasons worth of material," he confirmed. "We see it as having certain chapters that would enrich the overall story, but aren't necessary to tell the overall story. God willing, the network allows us the time to tell our complete story."
Fringe returns to Fox this Friday at 9/8c.