The Secret Avengers was the name given to Captain America and his fugitive allies when they were fighting against Iron Man, S.H.I.E.L.D., and the Initiative during Marvel's original Civil War. Later, Commander Steve Rogers resurrected the idea when he was the head of S.H.I.E.L.D. during Marvel's "Heroic Age." Steve believed the Avengers needed a covert operations wing and recruited Moon Knight, Black Widow, Beast, Valkyrie, War Machine, Nova (Richard Rider), Ant-Man (Eric O'Grady), and, later, Shang-Chi for the task. The team would go through changes before too long, with Hawkeye taking over and bringing Giant-Man, Agent Venom, the Torch, and Captain Britain into the fold. S.H.I.E.L.D. would take the idea later and form their own team consisting of Nick Fury Jr., Hulk, Mockingbird, Hawkeye, Spider-Woman, Black Widow, Taskmaster, Iron Patriot, and Quake.
This seems like an idea prime for adaptation in the Marvel Cinematic Universe, and, now that we are entering the next phase, there are plenty of ways that the Secret Avengers could be adapted into MCU.
10 Nick Fury Deems It Necessary
The most likely answer is also the most expected and, frankly, boring possibility. Nicholas J. Fury is the spymaster of spymasters. S.H.I.E.L.D. has been dismantled thanks to the machinations of Hydra, so it stands to reason that Nick Fury would want a new covert ops team at his disposal. More and more superheroes are popping up in the MCU, so he could easily recruit a team to function as his Secret Avengers to fight the more complicated threats that Nick doesn't want to battle out in the open. It's hard for the Avengers to have deniability and be global celebrities, so Nick would want a team with heroes nobody knows about.
9 It's How Sam Wants To Run Things
The door for Sam Wilson to become Captain America was left wide open at the end of Avengers: Endgame. Sam Wilson isn't from the same generation as Steve Rogers, and he worked for a different kind of military. His missions as a pararescue trooper were intended to be more stealthy by design, so it stands to reason that he would want to run an Avengers team that stays out of the spotlight. On top of that, Sam Wilson isn't the national celebrity that Steve Rogers was as Captain America. The public doesn't yet have the means or reason to know who the Falcon is in the MCU, so Sam may just decide to maintain some semblance of a secret identity and run a Secret Avengers team to match.
8 It's Just How The Avengers Operate Now
There's no reason that the formation of a Secret Avengers team should be a unilateral decision. Many of the presumably still-active Avengers are the more private ones: Ant-Man, Doctor Strange, Captain Marvel, the Falcon, Scarlet Witch, War Machine, and the Winter Soldier. Black Panther is the head of a nation, and even he has tried to separate the actions of the Black Panther from those of King T'Challa to the world at large. As such, the new incarnation of the Avengers may just naturally be a Secret one.
7 The Return Of Ronin
It is a possibility that Hawkeye will stick around for the Avengers going forward, and he may be the one to take the lead as one of the senior members. Clint Barton, after losing Black Widow and Iron Man, may decide to bring back the Ronin identity and lead a team of Avengers on more stealthy missions than the ones they've taken so far.
Given the presence of Ronin, these would also likely be far more bloody and brutal missions, so he would need a team that's okay with that: maybe War Machine, Valkyrie, and the Winter Soldier?
6 The Return Of Hydra
While Hydra seems to be thoroughly obliterated, we do know that Baron Zemo will be returning in the Falcon & The Winter Soldier television series. It is possible that we may see a resurgence of Hydra in the MCU. In that case, a Secret Avengers may be needed to quash this new incarnation of Hydra before it has time to grow and fester. This possibility would actually go with Nick Fury or Sam Wilson mandating a new Secret Avengers unit.
5 The Return Of The Defenders
This one feels particularly far-fetched, but it would be fantastic to see the Defenders return. Given that the Defenders themselves are largely private citizens working as street-defending vigilantes, it would stand to reason that they would want to be Secret Avengers—if they were to be Avengers at all. It would be a good way to bring Luke Cage, Daredevil, Jessica Jones, Iron Fist, and even the Punisher back into the fold.
4 Spider-Man Goes To Ground
With Spider-Man's secret identity exposed, it seems likely that the Web-Slinger will need to go on the run. Peter would need some people to watch his back in this situation. With that in mind, it seems possible that a new Secret Avengers team may naturally form around Spider-Man working as a nomadic superhero. It could even be inspired by the Ultimate Spider-Man television series, with the likes of White Tiger, Nova (Sam Alexander), and Amadeus Cho joining the team.
3 A Civil War Redux
Neither Avengers: Infinity War or Avengers: Endgame indicated that the Sokovia Accords have gone anywhere. The new Avengers team may need to be a Secret one if they don't want to be operatives for the United Nations. This also would jive with Spider-Man's secret identity getting exposed in Far From Home.
Luke Cage, Falcon, and Iron Fist were all part of Captain America's Secret Avengers team during Mark Millar and Leinil Francis Yu's Civil War story. The new Secret Avengers team could be an anti-registration one and settle the matter of the Sokovia Accords once and for all.
2 The Rise Of The Champions
A Secret Avengers team could also be a good way to introduce the Champions team to the MCU. Given that all of the Champions are younger heroes, it would stand to reason that they wouldn't want to be in the spotlight and risk themselves or their families. As such, they could help others and save the world from the shadows and avoid becoming massive celebrities in the MCU like the prior Avengers team. This would be a good way to introduce Ms. Marvel, Miles Morales, and Amadeus Cho.
1 This Is How We Get The Thunderbolts
The Secret Avengers could be just how we get anything like the Thunderbolts in the MCU. During the Initiative era of Marvel Comics, Norman Osborn's Thunderbolts functioned like the Secret Avengers analog for Iron Man's Mighty Avengers team. Baron Zemo, Abomination, Ghost, and the Vulture are all still kicking around in the MCU, and that's not a bad start for a Thunderbolts team. They could easily introduce the likes of Songbird, Atlas, Mach I, and Moonstone in the movie or series itself.