Most of Fury's story is classified; the rest you may simply choose not to believe.
War is Hell Nicholas Joseph Fury grew up so poor his parents couldn't even afford to send him to the School of Hard Knocks. He gained his education on the cruel streets of New York's Hell's Kitchen, a place that made the trenches of World War II look like a picnic at the beach. Nick found his way into those trenches and ended up being a sergeant in the US Army and leading a bunch of yahoos called the Howling Commandos. They saw a lot of fights and won a few, too, all the way across Europe and the Pacific.
By the time the war came to a close, Sgt. Fury's decorations for valour practically outnumbered the hairs on his head, but he didn't care; he just wanted the whole shooting match to be over. The big brass put him into the precursor of the CIA, the Office of Strategic Services, right after the war. Around that time Nick also found he wasn't really aging like normal folks, thanks to a little thing called the Infinity Formula.
Oh, and he took to wearing an eye-patch, too -- another gift from the war.
Spy Stuff From the OSS, Fury moved over to the new organization, the CIA, and gained a lot of experience in spying and covert operations. Tony Stark, the world's leading industrialist and weapons designers, convinced Fury to head up S.H.I.E.L.D., a government group that tackled big problems worldwide and had more resources and agents than an old soldier like Nick'd ever seen. He grew that office into a force to be reckoned with and targeted such terrorist teams as HYDRA and any other goofballs with world domination on their sick, twisted minds.
Fury's days with S.H.I.E.L.D. weren't always a bed of roses, and he suffered a lot of grief at its helm. But after every blow-up and every rebuilding, he always came back to the fold and got the job done. During his time there, he gained a clearance level that'd make anyone's head swim, and a knack for rooting out bad guys that'd put any so-called "superhero" to shame. S.H.I.E.L.D. swam in Nick Fury's bloodstream; he ate, drank and breathed it.
Alien Invasion There came a time when the entire Earth fell under a Secret Invasion by the alien shape-shifting Skrulls, and Fury went deep underground to fight back with a secret team of his own. When the whole mess went public and fighting broke out in the streets, Fury and his people struck from covert bases around the globe, a little S.H.I.E.L.D. detail most folks didn't know about.
When the final battle against the Skrulls went down, Nick Fury led the Young Avengers and the Initiative heroes against the invaders and helped turn the tide for Earth's defenders. Sadly, he also watched as Norman Osborn, the "former" criminal known as the Green Goblin, made the killshot that not only took down the Skrull queen but endeared him in the eyes of a desperate public. Osborn basically took charge of S.H.I.E.L.D. and its former commander faded back into the shadows, retreating underground again.
Darkest Before the Dawn With Norman Osborn in the spotlight and his H.A.M.M.E.R. forces play-acting like S.H.I.E.L.D.'s replacement, Nick Fury's world tumbled into an even deeper hole. Information that HYDRA secretly controlled came to light and Fury knew then he couldn't rest on his laurels and retire. He formed a new team, the Secret Warriors, and with a myriad of other covert operatives around the world waged war from the shadows against Osborn and his cronies.
The former Green Goblin's "dark reign" came to an end in a daring H.A.M.M.E.R. raid on the fabled city of Asgard, which then hung in the sky over a small American town. Fury and his people joined in on the fun and once again provided back-up to one of the biggest battles since the Bulge. With Osborn finally behind bars, Fury allowed Steve Rogers to take over running the whole spy network thing, but vowed to keep his one good eye focused squarely on any threats that might rise up to take away our freedoms.