The Marvel Cinematic Universe has had peaks and valleys in terms of characters that are largely heroic but have some dark sides. For example, Peter Parker nearly killed the Green Goblin after the murder of Aunt May. Meanwhile, Moon Knight wants to protect lives but does so with extreme violence. Essentially, there's always a dark side, even with heroes that always do the right thing. But perhaps the darkest moment of one character came from Nick Fury during Phase One of the MCU, and no one noticed.
Phase One was designed to establish many characters leading to their meet-up in The Avengers. As a result, each entry did a great job forming the base qualities of each hero before future installments would further explore their personalities. A great example of this was how, in Iron Man 2, Black Widow was a double agent for Fury but still fought for good. However, in the comics, Fury has had his own streak of using people for the greater good. While it may seem he wasn't as bad in the films, it was showcased in plain sight in Iron Man 2 and showed just how manipulative he could be.
Nick Fury Manipulated a Dying Tony Stark
In Iron Man 2, Tony Stark had to contend with fatal side effects from his chest Arc Reactor. While palladium was a viable power source, it didn't agree with his body and was slowly poisoning him. As a result, Tony was enduring a slow death that he tried to solve privately. However, he eventually accepted his fate until Fury showed up and told him he was needed to finish a project his father had started. The project in question was to create a new element with an equally viable self-sustaining energy source first introduced by Howard Stark.
This new element would continue to power Stark's suits and other buildings but was also the product of research Howard had done when he had his hands on the Tesseract. As it turned out, Fury needed him to solve the mystery because he was looking for a source that would match the Tesseract. But even though he likely wanted to do Tony a favor by helping him save his life, it's also likely that Fury wanted to find a secondary power source to power weapons should the Tesseract be unavailable again.
Nick Fury's Methods Proved His Unpredictability in the MCU
Fury is far from a bad man, but his actions are often controversial, as he's one to sacrifice one life to save thousands if the situation calls for it. Therefore, if Howard's creations couldn't save Tony and Fury knew, he likely would've presented it the same way to motivate the inventor. Because of this, it proved just how unpredictable Fury could be if the need arose while also showing how much he has evolved since he was director of S.H.I.E.L.D.
Tony's new element changed the world by offering cleaner energy and making his suits much more powerful. But the motivation came from a man who likely wanted the result for his own plans, and Tony's survival would be nothing more than a welcome perk. But, as The Avengers proved, Fury wasn't afraid to keep projects close to his chest, and even though he remains a hero, his limits to what he won't do are the biggest concern.