After three years' absence in the MCU, the Captain America: Civil War.
The answer seems to be that both Fury and Hill have allied themselves with an unknown organization. Their resources are clearly considerable; they have access to data from satellites that are actually monitoring Wakanda. But, while Fury is used to being in charge of S.H.I.E.L.D., he's not the boss of this new agency: the two refer to "Control."
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This would certainly explain why both Fury and Hill have gone missing. Until now, it had been assumed that Fury was working solo, while Hill was still working with Stark. Instead, it seems they've become field agents for another organization. This may actually explain why Fury didn't get involved with the chaos around the Sokovia Accords; no matter how much he wanted to, his bosses would be wary of the political fallout. But who are Fury and Hill actually working for? And how long have they been doing so?
Is This Actually S.H.I.E.L.D.?
It's important to note that the Russos are clearly continuing Fury's story from Age of Ultron. There, Fury and Hill came to the rescue during the climax of the Battle of Sokovia, working with a group of S.H.I.E.L.D. loyalists. One notable example was Cameron Klein, who's explicitly name-dropped during Infinity War's post-credits scene. Given that even saw Fury using a S.H.I.E.L.D. Helicarrier, could this actually be S.H.I.E.L.D.? It's true that Marvel's official tie-in TV series, Agents of S.H.I.E.L.D. has offered no hint that Fury is still involved with the resurgent organization, although that needn't be a barrier; the movies dictate to the TV shows, not the other way round.
But it would seem rather odd for Marvel Studios to reintroduce S.H.I.E.L.D. at this stage. So far as the movies have been concerned, S.H.I.E.L.D. were shut down in The Winter Soldier. To suddenly reintroduce them in an end-credits sequence would be a strange, disconcerting decision. It's notable that S.H.I.E.L.D. vehicles and devices have typically been emblazoned with the distinctive logo, and no such insignia was visible in the post-credits scene. Meanwhile, the showrunners of Agents of S.H.I.E.L.D. have begun tying into Infinity War, but haven't set up anything like this in Season 5.
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So Who Is Fury's Organization?
It seems more likely that we're dealing with a whole new organization, one that Fury began working with after leaving S.H.I.E.L.D. along with Hill and Klein. It's possible they were even working for this agency in Age of Ultron. Hill, for example, could easily have been placed undercover at Stark Industries to monitor the Avengers, and when things really began to kick off, Fury's bosses could easily have sent Nick to the Barton homestead in order to give the team a morale boost. He and Hill could then have been ordered to use whatever resources they could obtain to help out in Sokovia.
That brief post-credits scene doesn't give much information about the bigger picture. It does, however, confirm that Fury's interests intersect perfectly with this unknown group. He's able to use their resources to monitor Tony Stark, and their satellites are being used to observe former S.H.I.E.L.D. hotspots like Wakanda. While this organization is unlikely be a resurgent S.H.I.E.L.D., it does seem to have picked up S.H.I.E.L.D.'s old priorities and resources. Perhaps another spy agency used the collapse of S.H.I.E.L.D. to expand its remit and funding.
Of course, it's entirely possible Captain Marvel's imminent arrival in the MCU, not on exploring Nick Fury's backstory. With both Hill and Fury erased from existence, it wouldn't be much of a surprise if Avengers 4 simply ignored this spy mystery.
