3. The Superhuman Registration Act
The Superhuman Registration Act (SHRA) came about after the team of young heroes known as The New Warriors inadvertently caused an accident that resulted in an entire town being destroyed. The government went into full-on panic mode and in an effort to contain the hysteria, and Reed Richards and Tony Stark came up with the SHRA that called on all super-powered individuals to register with the U.S. government by law. This caused a big rift between the superhero community with Iron Man on the pro-SHRA side, and Captain America on the anti-SHRA side. Heroes fought one another, Captain America was killed on route to his trial, Norman Osborn was inexplicably put in charge of all superhuman activity in the US (including S.H.I.E.L.D. which Osborn renamed H.A.M.M.E.R.) and Skrulls nearly took over the planet. At the end of all of this nonsense a back-from-the-dead Captain America took Osborn's place and convinced the government to repeal the SHRA. So in the end it was like none of this stuff ever even happened. Yay Bendis! The Agents of S.H.I.E.L.D. could ignore a lot of the hero vs hero drama and instead focus on the enaction of SHRA and S.H.I.E.L.D. being tasked with enforcing it. Along the way Skye could hack into some S.H.I.E.L.D. computer she shouldn't be looking into and find out that a number of the super-humans being registered are also being held against their will and forced to serve as a super-powered army for a shadowy division within S.H.I.E.L.D. Maybe even Mike Peterson could be one of the super-powered being held against his will and Coulson and his team would then have to rescue these folks while also exposing the mastermind behind the shadow operation within the organisation.