Marvel Studios' Secret Invasion created many MCU plot holes over the course of its divisive storyline. After premiering on June 21, 2023, Secret Invasion concluded after six episodes on July 26, and the finale cemented the Phase 5 series as one of the lowest-rated MCU projects to date. Secret Invasion's controversial final episode came after weeks of minor mistakes, with the series perhaps creating more plot holes than any previous Marvel Studios project. Expected to be a stepping stone to The Marvels and Armor Wars, Secret Invasion's burning questions could be answered in future projects, as the series left a lot unanswered.

Featuring a stellar cast including the likes of Samuel L. Jackson, Cobie Smulders, Don Cheadle, Emilia Clarke, Olivia Colman, and Kingsley Ben-Adir, Secret Invasion was gearing up to be a strong addition to the MCU's Phase 5. However, the series has been met with criticism concerning the writing, pacing, and key story elements that perhaps didn't make much sense. When a rebellious faction of shape-shifting Skrulls threatens life on Earth, it seems only Nick Fury has the power to stop them, curiously without the inclusion of any of his superpowered friends. Secret Invasion created some major plot holes that Marvel Studios may spend several future projects correcting.

12 Replaced Humans Would Have Been Exposed To Radiation In New Skrullos

During Secret Invasion, it was revealed that a million Skrulls had assumed human identities and have been living covertly on Earth. This means that a million human bodies have been kept in stasis while the Skrulls have assumed their lives, and the humans that were replaced by the members of Gravik's rebellious faction of Skrulls were being held within the confines of New Skrullos. Situated in an abandoned Russian nuclear plant, these humans would have been exposed to severe amounts of radiation - as confirmed by Gravik when he invited Nick Fury to New Skrullos. This could have lasting repercussions on these humans, but this wasn't addressed in Secret Invasion.

11 The Skrulls Could Have Moved To Thanos' Garden Planet

The Skrull rebellion wanted to claim Earth as their own after Nick Fury and Carol Danvers failed to keep their promise of relocating the Skrull refugees after the events of 2019's Captain Marvel. It's unclear how hard Fury and Danvers worked to find the Skrulls a new home, as one suitable planet has already been seen in the MCU: Thanos' Garden from Avengers: Endgame. The Garden is capable of supporting life, is seemingly devoid of dangerous species, and is a vast and beautiful landscape that would have made a peaceful home for the Skrulls. Captain Marvel knew of this planet's existence but made no moves to relocate the Skrulls there.

10 Gravik & The Rebellion Kept Leaving Dead Skrulls Everywhere

Gravik's plan to claim Earth as a home for the Skrulls was flawed in many ways and far too complicated, but one of its major scruples was the fact that he didn't make much effort to hide the fact that it was the Skrulls causing devastation. Gravik's plan involved pitting Russia and the United States against each other, hoping to incite World War III. However, while masquerading as both Americans and Russians, various Skrulls were killed - reverting to their natural forms - only to be left on battlefields. This would have been a dead giveaway that neither the Americans nor the Russians were attacking, but a nefarious alien species.

9 G'iah Is Too Overpowered After Secret Invasion's Finale

After the Harvest was introduced in Secret Invasion episode 5, a vial of the collective DNA of many MCU characters, Gravik and G'iah used the serum to enhance themselves into Super Skrulls in Secret Invasion's finale. After a massive CGI battle, G'iah dispatches Gravik with her newfound abilities, including those from the likes of the Hulk, Ghost, Mantis, and Captain Marvel. G'iah's incredible range of new powers clearly makes her the MCU's most overpowered hero, which will be a hurdle that Marvel Studios must address in the future, as her involvement in any battle would be an incomprehensible advantage to the MCU's heroes.

8 The Skrulls Replacing Rhodey Doesn't Make Sense

One of Secret Invasion's biggest shocks came when James "Rhodey" Rhodes, a.k.a. War Machine, was revealed to be the Skrull Raava in disguise. Though it's unclear exactly how long Raava had been masquerading as Rhodey (potentially after Captain America: Civil War), the fact that it was Rhodey who was replaced has led to some confusion. If the Skrulls were going to infiltrate the Avengers, surely it would have made more sense to replicate a more high-profile member, such as Sam Wilson's Captain America, Natasha Romanoff's Black Widow, or even Nick Fury himself. Rhodey's replacement seemed inconsequential though will surely be discussed further in Marvel Studios' upcoming Armor Wars.

7 Nick Fury Could Have Ended The Skrull Rebellion By Calling The Avengers

One of the most confusing aspects of Secret Invasion was Nick Fury's insistence that the Avengers needn't be called to action. The Skrull rebellion posed a threat to all human life, which would certainly necessitate the intervention of the Avengers, but Fury was adamant about facing the Skrull rebellion alone, not even bothering to call his superpowered friends, even after it became clear that one of the Avengers had been replaced by a Skrull. Marvel Comics' Secret Invasion event included most of the Marvel Universe's heroes battling the Skrulls, but Marvel Studios' version completely omitted any superhero action, which simply didn't make sense.

6 Gravik's Plan Was Far Too Complicated

Secret Invasion's most obvious plot hole was the explanation of the Skrull rebellion's actual plan of world domination. Masquerading as American terrorists and then Russian soldiers, Gravik and his warriors wanted to incite nuclear war, eradicating humanity and allowing the Skrulls to claim the Earth as their own. This was a very complex plan that could have been simplified had the Skrulls utilized their sole power: shape-shifting. The Skrulls could have transformed into someone capable of simply flicking a switch and causing nuclear strikes, and Rhodey had several opportunities to assassinate President Ritson, but the rebellion continued with their convoluted plan nonetheless and ultimately failed.

5 Aliens Are Already Living Peacefully On Earth, So Why Can't The Skrulls?

Everybody in Secret Invasion seemed to be under the impression that an alien species wouldn't be accepted into society, meaning the Skrulls either needed to rebel or move off-world. However, there are already aliens living among humanity on Earth. After the destruction of Asgard, Thor and his people set up a new home on Earth, now dubbed New Asgard, which has become a popular tourist destination. She-Hulk: Attorney at Law also proved how accepting humans had become, as the existence of shape-shifting Light Elves was common knowledge. With heroes like Thor and the Guardians being celebrated, there's no reason another alien race wouldn't be allowed to live peacefully on Earth.

4 Captain Marvel Couldn't Find A Single Suitable World In Thirty Years

Captain Marvel, set in 1995, introduced the Skrulls to the MCU and brought them to Earth for the first time, ending with the promise that Fury and Danvers would find the Skrulls a new home. Secret Invasion was set in 2025, thirty years later, and revealed there had been no progress. While this task may have been difficult for Fury, and he evidently had an ulterior motive for keeping the Skrulls on Earth, Captain Marvel surely would have come across a safe world for the Skrulls in those thirty years. Exactly what she was up to in her absence is a question that must be answered in 2023's The Marvels.

3 Maria Hill & Talos' Secret Invasion Deaths Are Meaningless

Secret Invasion shocked audiences right out the gate by featuring the tragic death of Cobie Smulders' Maria Hill at the end of episode 1. Killed by Gravik in disguise as Nick Fury, this would have been the perfect moment to incite revenge from the former Director of SHIELD. Add to that the murder of Ben Mendelsohn's Talos in Secret Invasion episode 4, and the battle between Fury and Gravik was gearing up to be an epic and emotional spectacle. However, this never happened, as the series' final battle saw G'iah take on Gravik, meaning both Talos and Maria Hill's deaths (Hill in particular) saw no resolution and were effectively meaningless.

2 Some Of The Harvest's DNA Samples Don't Add Up

Nick Fury revealed that DNA samples had been collected after Avengers: Endgame's final battle and combined to form the Harvest. Secret Invasion's finale revealed whose DNA was included in the Harvest, but some of the samples didn't make sense. Thanos and his army (and all remnants of them) were snapped away by Iron Man in Endgame, so the Mad Titan's, his Black Order's, the Outriders', and the Chitauri's DNA wouldn't have been available. Others such as Ghost and Abomination weren't even involved in the Battle of Earth, so it seems these DNA samples were only included to provide familiar names for audiences rather than actually making sense for the story.

1 Secret Invasion Never Answered When Rhodey & Everett Ross Were Replaced

Perhaps the hottest topic of discussion surrounding Secret Invasion is the question of when Martin Freeman's Everett Ross and Rhodey were replaced by Skrulls. Rhodey's recent MCU appearances include Avengers: Infinity War, Endgame, and The Falcon and the Winter Soldier, though Ross appeared more recently in Black Panther: Wakanda Forever, but it's unclear whether either character was a Skrull in these projects. It was expected that Secret Invasion would reveal these secrets, but this didn't happen. This is certainly one of the biggest mistakes made in Secret Invasion, as the series could have explored the magnitude of the Skrulls' infiltration on a much more emotional level.