The official prelude of Captain Marvel Comic has revealed that Nick Fury isn’t working for SHIELD! When Fury and Maria Hill return in the Infinity War post-credits scene, most viewers thought that it was pointed to a resurgent SHIELD but that’s not really the case.
The assumption was understandable, given that they all seemed well-organised right down to having a satellite to monitor Wakanda. If this wasn’t SHIELD, then it could be an organisation that had taken over SHIELD’s resources. There’s also a reference to “control” which seemed to reflect a certain structure of hierarchy. Fury and Hill both appeared to be Agents, working for a boss.
However, the prelude to Captain America reveals that all these assumptions were incorrect and Hill and Fury aren’t working for a new spy agency. Instead, they are operating independently, making use of resources Fury had hidden away while he was SHIELD’s director. Fury is a man of a lot of secrets and it seems he only stepped back into the light to get the Avengers back together.
There’s also a reference to Klein, a SHIELD loyalist seen in Captain America: Winter Soldier and Age of Ultron. Klein works for Transpo, a company suited to cover his tracks. Fury also gives away a reference to Colonel Rhodes, which proves that he had been in touch with War Machine. It’s still unknown who “Control” was but it could be a reference to Klein or even Avengers staff.
This comic tie-in does answer a major question, it also raises many for next year’s Spider-Man: Far From Home where Fury and Hill will be seen doing cameos. Spider-Man has also been seen in a “stealth suit” which was given to him by SHIELD in the comics during the Secret War storyline. If this happens, then fans might get to see SHIELD back in action after the events of Avengers 4, with Hill and Fury returning to the organisation.