SHIELD Academy was founded by an organization called SHIELD. The basic idea was to train extraordinary children, prodigies, to reach their maximum potential, and, eventually, become SHIELD's top field agents. As a military intelligence organization, SHIELD needed the very best of the best to work for them. They had been keeping an eye on America's youth for some time now, looking for potential future agents. The idea of approaching them with an offer to train them for that specific purpose was Howard Stark's idea.
Tony, being Howard's son, was naturally among the first to be recruited. He accepted immediately, partially for the unique educational experiences offered, but mostly just to get his dad's attention. His father had been obsessed with finding Steve Rodgers, a frail little wisp of a kid who had volunteered to be cryogenically frozen during World War Two. The plan was to thaw him out in a couple of years, but unfortunately he had been lost. No one was quite sure how, only that Hydra had somehow been involved. Since then, Howard had been searching all over Europe for the kid, desperately looking for his long lost friend. He had not exactly spent a lot of time with Tony, neglecting his duties as a father in favor of more time spent searching for Steve. Tony was determined to get his father's approval.
Clint Barton was recruited when he was fourteen. He had run away from an abusive family at an early age, and joined the circus. He had spent the next five years training as an archer for the circus and being homeschooled by the circus's performers. Working under the name Trickshot, he became quite a popular act. A SHIELD agent attending the show saw his performance and approached the circus's owner about recruiting Clint. SHIELD wanted him as a sniper. Clint, realizing this may have been the chance at a better life he was hoping for, accepted. His first assignment as a junior agent was to root out a mole.
Natasha Romanov was that mole. She was only seven when she was planted as a sleeper agent in the US during the last days of the Cold War. When the USSR fell, the Red Room, a group that trained little girls to be spies, did not fall with it. Instead they continued to operate in secrecy, and sent Natasha to live in the United States. She was fifteen when Clint found her. Fortunately for Natasha, the Red Room had dissolved by then, leaving her stranded in a foreign country. Taking pity on her, Clint made the call to recruit her, rather than ending her life.
Bruce Banner was sixteen when he was recruited. Well, recruited wasn't really the right word. It was more like he was forced to join. Sure, they gave him a choice. He got to choose between joining SHIELD and going to prison. Why? He'd tried to blow up his school with a gamma-bomb he'd built himself. It had taken him weeks of careful preparation, only to be discovered at the last minute by the school's janitor. Fortunately for him, SHIELD had been sufficiently impressed that they decided to recruit him rather than arrest him. His exposure to the gamma-bomb's radioactive fuel had destabilized his DNA, however. He probably would have died in prison if he hadn't accepted their offer. Instead he received the medical treatments that saved his life.
Thor was banished from Asgard, for sheer hubris, to live among the mortals on Midgard, Earth, during the summer of 1998. It was just a few months after Bruce had joined SHIELD, and the news was still abuzz with gossip about the failed gamma bomb attack. Thus, when Thor appeared amid a flash of lightning alongside a hammer that no one else seemed able to lift, very few people paid any attention. Those that saw it were dismissed as liars or crazy people by others. Except SHIELD, who immediately swooped in to scoop up the world's first alien visitor. Who looked an awful lot like a regular human teenager. Most teenagers couldn't bench-press small cars, however.
T'Challa ended up in SHIELD custody by way of a tragedy. 1999 was a cause for most people to celebrate. The turn of the millennium was fast approaching, and a lot of people took that as an excuse to party hard. To the people of Wakanda, it marked the beginning of a schism. The Jabari tribe had recently taken up the White Gorilla cult once again, and a tribal war broke out. During the chaos T'Chaka, the king of Wakanda and T'Challa's father, was killed. T'Challa was in the United States at the time, studying as an exchange student in an American high school. When his father was killed and the throne usurped, T'Challa was forced to stay in the US to avoid being killed by the new king, M'Baku.
How the six of them ended up being friends no one seemed really sure. It might have started with Tony and Bruce discussing science in the library after Bruce loaned Tony a book. It might have started with T'Challa and Thor realizing they were the only two who didn't really understand modern American pop culture. They ended up sitting together at lunch, the only two who didn't have friends to sit with. Natasha and Clint were already besties by that point. Natasha took pity on them, and invited them to sit with her and Clint. Tony and Bruce ended up at the same table when Tony noticed a new clique forming and decided to insert himself and Bruce into it. At least they wouldn't be part of the "nerd" clique anymore.
It was just the six of them at first; going to school like regular kids. Hanging out at the mall after school, playing video games in the arcade, watching movies at the theater. Even though they were part of SHIELD, life seemed fairly normal. They were just semi-average kids living an average life. Even T'Challa and Thor fit in fairly well, despite being from a different country, or a different world. After a while, they got used to their life in the US, and they fell into a pattern. Every day they did the same basic things: go to school, do home to do homework, then go out to have some fun at the usual hangouts.
All of that began to fall apart after the new kid showed up.