WARNING: The following will discuss major spoilers in Captain America: Civil War, anyone who has not seen the film yet and do not want to be spoiled should stop reading from this point on.
Captain America: Civil War, like the previous Captain America films, has had a profound impact in the Marvel Cinematic Universe (MCU). The biggest fallout from the deteriorated relationship between Steve Rogers/Captain America and Tony Stark/Iron Man being the disintegration of the Avengers team.
Naturally, we cannot expect this situation to last in the MCU. Despite the world’s animosity towards superheroes, it does need a superhuman team to take on the larger-than-life threats. What will likely happen in between this film and the next Avengers film is that the team will be reformed. As to who will make up the new Avengers is open for speculation.
New Avengers and Fugitives
But if the Marvel Studios films loosely follow what happened in the comic books then there might be two teams of Avengers in Avengers: Infinity War, Part I (at this point we don’t know what the film’s new name will be so let’s call it by its original title for now). In the Marvel Comics following the Civil War mini-series there were two Avengers teams, one was known as the Secret Avengers and operated outside the law and there was the “official” Avengers, which was later infiltrated with nefarious sorts and morphed into the Dark Avengers.
Avengers: Infinity War could roughly follow this development by having Tony Stark leading a new team composed of Vision, Wonder Man (Nathan Fillion will cameo as Wonder Man’s civilian identity of Simon Williams in Guardians of the Galaxy, Vol. 2, so he is a natural to play Wonder Man–a casting decision we foresaw years ago), a new Captain America, Captain Marvel (someone that the film’s directors, Joe and Anthony Russo, have suggested may appear), and someone new to the MCU perhaps She-Hulk or Tigra or even Black Knight.
Now the film could be about how the official Avengers are treated as celebrities, but the reality is that many of the new recruits are traitors. Think about it. This plot twist would be a variation of the Thunderbolts’ first storyline and Wonder Man’s initial appearance. When Wonder Man first joined the Avengers he was supposed to betray the team but had a change of heart and became an actual hero. The original Thunderbolts team was actually Baron Zemo and his Masters of Evil, who were pretending to be heroes. This twist could be unveiled to audiences who would be shocked that new recruits like Tigra or Black Knight are actually supervillains and Zemo was behind the scenes plotting this machination much like he did in Captain America: Civil War.
Meanwhile, Steve Rogers could adopt a new identity as either Nomad or the Captain as he did in the comic books. He would be without his shield, which he abandoned at the end of his third film. The new, evil Captain America (who can be Johnny Walker, the future U.S. Agent) could be the one wielding the shield while Rogers could use an energy shield like the one that Phil Coulson used in a recent Agents of S.H.I.E.L.D. episode. Of course, by the end of the film Rogers will rightfully regain the real shield. It could be given to him by Stark as a symbolic way of renewing their partnership.
Before that happens, Rogers will probably be leading his own clandestine team made up of Scarlet Witch, Black Widow, Ant-Man and the Wasp and Falcon.
Accords & Aftermaths
So, Secret Avengers, Dark Avengers, what does any of this have to do with Thanos and the Infinity Gauntlet? 
Perhaps Thanos’ team of the Black Order could show up on Earth looking for the final Infinity Stone, which happens to be embedded on Vision’s forehead. The aliens defeat the Avengers and take the Stone or are behind the betrayal. This would lead Stark and Rogers to realize they have to join forces to combat Thanos and the film ends. Cue the post-credits scene with a triumphant Thanos and his completed gauntlet.
OK, so what about the rest of the MCU? How does Captain America: Civil War affect it? To be honest, it may have minimal impact outside of the third Avengers film and the Black Panther solo film, and the reason can be seen in the lineup of films between Captain America: Civil War and Black Panther.
Up next is Doctor Strange, which seems likely to be set apart from the traditional MCU. Unlike Ant-Man, do not expect to see an Avenger making a cameo in Doctor Strange. At best, there may be a reference to one of the Infinity Stones. The same situation will apply to Guardians of the Galaxy, Vol. 2. That sequel takes place in outer space and according to director James Gunn, doesn’t have anything to do with Thanos.
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