I'm not even sure if I should post this. It's one of the oldest things I've written and therefore cheesier than macaroni & cheese. Also, I know this idea has been done before and there's one story in particular I read that inspired this but I can't remember what it was. I've looked for it but I can't find it. (If you are the author of a similar story, PM me so I can see if it's the one I'm thinking of and I can credit you.)
SHIELD had a secret that was carefully guarded and preserved. Only a handful of individuals had ever known it and most of them were dead. Fury knew it. Fury kept it. Passed down from director to director, it was buried in obscurity to the point of nonexistence. So well was it preserved that there was not even a whisper of it. No legend, no hints, no office gossip. It went from mouth to ear and never beyond. It was a secret that affected the security of the world and for that reason it was so zealously kept.
Project: Rebirth was never shut down. The first successful experiment promised that the process was possible. Too many resources had gone into the program for it to be closed, simply because the top researcher had been assassinated. The work went on. Vials of serum-infused DNA, extracted from the test subject, were stored and studied in undisclosed locations all across the country. Long after the war had been won and the country sequentially mourned and forgot their hero, efforts were put forth to reproduce the serum and its intended results. Most experiments ended in disaster. But some did not.
In 1969, Howard Stark's wife was pregnant. A prominent figure in the founding of SHIELD itself, Stark was able to procure for himself a sample of the coveted blood. The day arrived for the child's birth and once the labor had been completed and the mother sleeping soundly, Stark ordered his personal physicians to inject the infant with the serum. Anthony Stark was the first human being to be given the serum since Steven G. Rogers, three decades earlier. Without the Vita-Rays power, the effects were mental rather than physical. Though small in stature, the young Stark quickly surpassed his mentors, tutors, teachers and peers in intelligence. Eventually, his knowledge and electrical proficiency outpaced that of his father. The serum had latched onto the genetic affinity for engineering and enhanced it to astronomical levels. It was only the serum's rapid reproduction of cells which enabled Anthony Stark to survive the implantation of the Arc Reactor device.
Twelve years after Stark's infusion, SHIELD, much encouraged by the results exhibited by Anthony Stark, determined it would be profitable to move their own research forward from the theoretical to the practical. Clint Barton, a child, was selected. The injection appeared to have been a success. However, before more tests could be administered, Barton escaped SHIELD custody and was lost for many years. It was not until urban chatter of a legendary circus performer surfaced that SHIELD was able to recover their lost subject. In the time elapsed since his injection and retrieval, Barton's skill as a marksman had become remarkable. His vision had been selected by the serum as the characteristic which was to be increased.
America was not the only country to seek the serum for her own use. Through espionage and betrayal, many of her enemies obtained the serum in various stages of research. Most notably, the Soviet Union used her illegally acquired sample to produce her deadliest assassin. Having previously received paramilitary training from a young age, Natalia Romanova's skills became unparalleled. The serum increased her natural speed and agility. With the same blood flowing through his veins, Barton was dispatched by SHIELD to dispose of the threat of another enhanced human. Barton's insubordination turned their greatest rival into their greatest asset.
SHIELD did not stop at human testing. When an alien was discovered in the New Mexican desert, the organization took the opportunity to asses the serum's potency on other organisms outside of homo sapiens. The creature, later identified as Thor of Asgard, was easily subdued and SHIELD scientists were transported, along with the serum, to the location of the desert base to perform the infusion. The alien was released and surveillance posted to observe any and all effects. Body already transcending that of humans, the serum amplified the alien's inward sense of dignity and honor.
Outside of any government or organization, several scientists attempted to reproduce the serum through their own efforts. The results were overwhelmingly fatal. But in one case, the outcome was different. Dr. Bruce Banner transformed himself, through gamma radiation, into a beast such as had never before been seen. Unclassifiable and uncontrollable, Banner's monster laid waste to much of New York City before disappearing from the public eye. Aware of the danger posed by such an abomination, SHIELD maintained a careful watch over Banner.
When the alien known as Loki threatened the safety of the Earth, SHIELD gathered its army of super soldiers and pitted them against the incoming extraterrestrial menace. Under the leadership of the original recipient of the serum, the Avengers defeated their foes and secured peace for the world.