When you're Spider-Man for some time, Nick at one point believed the teenage wall-crawler had finally snapped and began to outline a plan to de-power, contain and, if necessary, kill the young Peter Parker before he became the next big supervillian. Working on the plan behind the scenes, the events within the massive "Clone Saga" storyline gave him reason to set it in motion, further adding to the overwhelming circumstances that Peter Parker was dealing with at the time.
In the Tinkerer, who agrees to work for Fury in lieu of jail time. Part of that work meant surrendering all of his technology, especially the ominous Slayer robot.
In the massive "Clone Saga" storyline, Fury learns about the illegal Peter Parker clones that began to appear and seeing an opportunity to contain the situation, he shows up to Peter's house in Queens with a massive army of armored SHIELD agents and robots later confirmed to be the Ultimate Spider-Slayers, developed from Mason's technology. While Fury's presence causes Gwen Stacey's clone to transform into Carnage and attack, Mason's communication with Fury reveals that Spider-Slayers were built "to slay a Spider" and their weapons had been calibrated to attack their targets' DNA. When Peter attacks Fury in hopes to defuse the situation and save his dying aunt, the Spider-Slayers' blasts floor Parker with Fury warning him to stay down and that his time as Spider-Man was over, threatening to paralyze him for good if he got up again.
When Fury and his forces confronted Peter and his wayward clones later at the ruins of Oscorp, the true mastermind of the situation is revealed to be Otto Octavius, Peter's old enemy whose work actually created the clones. While one of Fury's sentries was regrettably forced to kill one of the clones, Fury refused to take orders from Octavius and had his soldiers and the Spider-Slayers leave so Peter and the clones could have a talk with the former Doctor Octopus. When all was said and done, Fury still wanted to arrest and detain Peter, requiring the Ultimates to back him up as he continued to clash with the Fantastic Four and others who tried to convince him of Peter's innocence.
It wasn't until Mary Jane Watson, Peter's girlfriend and victim of the night's circumstances, told him that Peter looked up to Fury like a father and that despite everything, he still wanted to be a hero and eventually the Ultimates with Fury. Nick would later visit Peter at the hospital where his Aunt May was recovering and itted he was wrong. He had created the Spider-Slayers and the entire plan because he was afraid Peter had finally cracked under the stress of being Spider-Man. Convinced of Peter's heroism, Fury lets Peter keep his powers and continue to be Spider-Man. This proves that while Nick Fury could be a cold, calculating. manipulative authority figure, he was still human and could be wrong occasionally. Confirmation that Nick Fury has a heart has been deemed classified.
