Peter Parker will find himself in conflict with Nick Fury in Spider-Man: Homecoming, but in the sequel it's Samuel L. Jackson's Nick Fury and Cobie Smulders' Maria Hill.
Last year's official Captain Marvel Prelude explained just Avengers: Age of Ultron, who now works for a firm called "Transpo" and covers Fury's tracks. But now Fury's finally encountered a threat too great for him to beat, and as a result he's called on the one superhero he can track down; Spider-Man.
Speaking to Screen Rant on the set of Spider-Man: Far From Home last year, executive producer Eric Carroll revealed that the dynamic between Fury and Peter will be very different to the mentor/father-figure relationship Spider-Man had with Tony Stark. As he explained:
"One of the themes we wanted to play with was youth. It's the timeless theme of these coming of age movies. Why do adults operate in the grey? Spider-Man is like, "This is easy. Let's just do the right thing" or "Let's just tell people what's going on and everyone will be okay" and Nick Fury's like, "That's not how the world works, kid." So, he just gets wrapped up in this sort of spy adventure, being driven by Fury and getting more-and-more caught between how he wants to operate and how he's being told he should operate."
Nick Fury is used to operating from the shadows, trusting nobody, and getting his own way. His morality is always shades of grey. In contrast, Spider-Man is a teenager who's used to working out in the open, with a much more concrete sense of right and wrong. Where Peter adored Tony Stark, and loved working with him, he's going to find himself much more conflicted about being a part of Nick Fury's operation. As Carroll noted, "We've got Peter Parker, the young optimistic hero and then you've got Nick Fury, this cold war-era super spy. And their ideologies can't help but clash."
Spider-Man starts out with only a little knowledge of Nick Fury, "through urban myth and talking to guys like Tony," but he gets something of a primer from Happy Hogan early on in the film; presumably that's the scene from Mysterio to the team as someone experienced with the threat of the Elementals. But he feels he wants Spider-Man on board as well.
Ironically, it's entirely possible Fury and Hill will come to regret that decision. Carroll hinted that the relationship between Spider-Man and Fury will deteriorate over the course of the film, with Peter Parker coming to question Nick and decide to operate on his own. He accepted Tony Stark as a mentor and father-figure; but it looks as though Nick Fury will be rejected.
