5 Big Twists We Want To See In A MCU Secret Invasion Storyline
Earth's Mightiest...Aliens?

One of the first things that we (and most fans) want to see from a MCU version of "Secret Invasion" is the reveal that some of the Avengers we've been following since Phase 1 are actually Skrull operatives.
In Marvel Comics, the first hints of the Skrull invasion are found when a Marvel hero (Elektra) dies in battle, and reverts back to her natural Skrull form, revealing the swap-out deception. If Avengers: Infinity War truly sacrifices some Avengers' lives to beat Thanos, it would be a perfect epilogue to find out that one of the heroes we're mourning over wasn't actually a hero at all.
Of course, in the comics, the Elektra reveal was used by a different Skrull agent (Spider-Woman) to gain the Avengers' trust, further undermining them. It would be great if the reveal of one Avenger and/or S.H.I.E.L.D. agent Skrull in the MCU, only led to the reveal of many others hiding in the ranks.
More: Are Some Avengers Already Skrulls?
prevnextNick Fury's Secret Warriors

In Marvel Comics, Nick Fury is one of the first leaders of the Marvel Universe to realize The Skrulls are infiltrating positions of power, in order to launch a full invasion. Fury had been removed as director of S.H.I.E.L.D., but he still had a battle plan to carry out: the super-spy tracked down superpowered family members of second-tier villains (plus a few of his own hand-picked operatives) and trained them to be a strike team of "Secret Warriors," who would be overlooked by the Skrulls, and ergo safe from being replaced.
The Marvel Cinematic Universe needs some new blood after Infinity War, and the movie and TV sides of the MCU could stand to be linked closer than they traditionally have been. Nick Fury's Secret Warriors would be a great way to bring the characters of Agent of SHIELD and some MCU movie heroes together, in a storyline that could crossover between the big and small screens.
Captain Marvel will already lay groundwork for Fury knowing about the Skrull threat; so having the S.H.I.E.L.D. Director make his usual eleventh-hour return (with a badass team behind him) would be fittingly epic, after his long absence.
The Super-Skrulls

One of the most famous Skrull characters is Fantastic Four nemesis the Super-Skrull (Kl'rt), who is (ironically) one of the reasons that Fox had rights to the Skrulls for so long. In the "Secret Invasion" story, The Super-Skrull ranks were expanded to include a new breed, who each were endowed with the powers of multiple Marvel heroes, in some devastating and deadly combinations.
The new Super-Skrulls were formidable opponents for the Marvel heroes fighting against the Secret Invasion - and they would be excellent henchmen in a MCU version of the story. Since there are multiple Super-Skrulls, they could show up anywhere (in the TV series and movies), offering vary levels of threat, depending on who they are fighting.
Seeing the powers of Marvel superhero and villains in live-action has been exciting; seeing Super-Skrulls use multiple powers at once, and functioning as single-soldier armies, would be next level!
prevnextEvil Twin Action

It goes without saying that if the MCU was going to adapt a story like "Secret Invasion," then one of the main features would be seeing the heroes take on "evil twin" versions of themselves, or those close to them.
This is another aspect of the Secret Invasion that's easily doable in any show or film included as part of the storyline. It's also a great way to keep suspense up, as seeing seemingly trustworthy characters suddenly betray and/or kill their allies would keep both the characters and viewers wildly off balance.
Finally, Marvel loves to push the visual effects of its MCU projects, and having an actor appear onscreen as both the "good" and "evil" versions of themselves, for an epic throwdown, would be a good way to spend the budget. Entire teams of copycat combatants? Even better.
prevnextThe Dark Reign

While The Skrulls eventually lose the military campaign against Earth and its heroes, the aliens' long-term campaign of subversion and psychological manipulation turns out to be a rousing success. When the "Secret Invasion" is over, there is a thick cloud of distrust still hanging over the Marvel superheroes. Tony Stark is discredited for allowing the invasion to happen, and S.H.I.E.L.D. is dissolved and deemed ineffective, by government order.
Into the void left by The Avengers and S.H.I.E.L.D. steps Norman Osborn/Green Goblin, who becomes head of S.H.I.E.L.D.'s successor, H.A.M.M.E.R. Osborn uses his influence to give Marvel supervillains new levels of access and legal leeway, by refitting and posing them as superheroes. The Marvel Universe then entered a period of supervillain dominance known as the "Dark Reign" storyline.
If "Secret Invasion" is the next big MCU storyline, then fans would naturally want to see "Dark Reign" as its followup. And with films like Spider-Man: Homecoming already setting the stage for it, the MCU villains getting their own Dark Reign chapter seems like an easy (and fan-approved) twist to pull off.
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