The subject of this article pertains to a reality with no official designation, so it has been assigned a Temporary Reality Number. (For more information on TRNs, go to this page).
A group of rogue S.H.I.E.L.D. agents were able to frame Director Nick Fury for the murder of an alternate version of Spider-Man. After being taken into custody, he escaped and created the Secret Warriors. Together, they weeded out the traitors, allowing Fury to retake the mantle of S.H.I.E.L.D..
Spider-Men
When the Sinister Six created a portal that allowed them to enter Earth-TRN461, S.H.I.E.L.D. was able to utilize the portal to create a team of Spider-Men from across the Multiverse to stop them.
Civil War II
After the implementation of the Superhuman Registration Act, Spider-Man II convinced Fury to register with him. Fury sent agents to apprehend anti-SRA heroes, the Secret Avengers, but the snipers shot Agent Venom. Almost having caused the death of the hero, Nick stopped pursuing the Secret Avengers.
Symbiote World
After Spider-Man disobeyed Fury's order to disband the Spider-Force, he assembled a squad a S.H.I.E.L.D. agents to force them to disband and leave Klyntar.[1]
Notes
Nick Fury believes there may be a mole in his organization.[1]