Writer Brian Michael Bendis stated in interviews that the motivation for the invasion is the destruction of the Skrull Empire in the Annihilation storyline. Bendis said the Skrulls believe Earth "is religiously and rightfully theirs," and that there are hints as to the plot placed in the limited series Secret War and the title New Avengers from the first issue. The limited series concluded the plot and was, according to Bendis, "a hell of an end."
In November 2007, several ongoing titles and mini-series were branded as tie-ins to the main Secret Invasion storyline, with the tagline: Secret Invasion: The Infiltration. In addition to the core story, the Avengers titles provided additional plot material and acted as a link between titles. Other Marvel titles also featured variant covers with the characters depicted as Skrulls. Bendis stated that the series would not deal with the origins of the invasion, but is conceived from the following perspective: "If there's a character on the team who's a Skrull, we will rewind from when they got on that team, or from before they got on that team, so when they are infiltrated, how they became who they became and the effects of their actions from their 'point of view' is shown."
The Marvel website featured two online-exclusive e-comics for the event, titled Secret Invasion Prologue (a seven-page comic that reveals the replacement of a previously unknown Skrull agent) and Secret Invasion: Home Invasion (a MySpace video blog featuring a young teenager named Kinsey Walden and her fears regarding her brother's strange behavior), supported by comic pages by writer Ivan Brandon and artist Nick Postic.
After the Kree-Skrull War a group of Earth's superheroes—Iron Man, Mister Fantastic, Namor, Black Bolt, Professor Charles Xavier and Doctor Strange—band together as a group called the Illuminati to secretly confront the Skrulls. They attack the Skrull Empire, and warn that any further invasion attempts of Earth would mean further reprisals. However, they are all captured and intensely studied before escaping.
An eventual successor to the Skrull throne, Princess Veranke, claims that a prophecy foretold the annihilation of the Skrull homeworld. The current Emperor, Dorrek, exiles her to a prison world for inciting religious extremism. After the destruction of the Skrull Throneworld by the cosmic entity Galactus, Veranke becomes Empress by lineage, and guides an invasion of Earth, armed with the knowledge of superhumans gained from having studied the Illuminati. The Skrulls capture several superhumans and infiltrate Earth's defenses, with Veranke herself posing as heroine Spider-Woman. Veranke, however, is inconvenienced when there is a breakout of supervillains at the Raft prison, which forces her to join the New Avengers team.
Elektra, the leader of the ninja group the Hand, is revealed to be a Skrull named Pagon after dying in battle with the New Avengers. Veranke takes the corpse to Tony Stark to sow distrust among the superhero community. She joins the Mighty Avengers, claiming it will throw the Skrulls off balance. Posing as agents of spy organization S.H.I.E.L.D., the Skrulls attempt to mine the metal vibranium in the Savage Land and battle the New Avengers before being killed. The Illuminati battle an impostor posing as Black Bolt and two new Super-Skrulls, possessing all-new powers.
The Skrull invasion destabilizes the superhuman community as:
- Simultaneous strikes disable the S.H.I.E.L.D. Helicarrier and orbiting base The Peak.
- A breakout is instigated at the supervillain holding facility the Raft.
- The Baxter Building headquarters of the Fantastic Four is transported to the Negative Zone.
- The Thunderbolt Mountain headquarters of the Thunderbolts is attacked.
Additionally, the Avengers are attacked by Skrulls posing as heroes in the Savage Land, and Reed Richards is wounded by the Skrull Criti Noll (who was posing as Henry Pym) seconds after determining a way to identify the shape shifters.
After several battles between Earth's heroes and the Skrulls in Manhattan and the Savage Land, Mr. Fantastic manages to develop a device that can detect the aliens. Criminal kingpin the Hood aids the heroes, deciding that "no more Earth is bad for business." Veranke regroups with her forces in New York, and a final battle against the combined Avengers (now aided by Nick Fury and his new Commandos, Thor, Daredevil, Ka-Zar, and super teams the Young Avengers and the Thunderbolts).
In a final battle, Veranke is wounded by the Avenger Hawkeye. Criti Noll activates a booby trap placed on the heroine Wasp, although the blast is contained by Thor at the cost of her life. Veranke is then shot and killed by Norman Osborn (using a weapon he created with intelligence stolen from Deadpool). The last remnants of the Skrull armada are destroyed, with Iron Man locating the missing heroes. S.H.I.E.L.D. is dissolved by executive order of the President of the United States while a last Skrull (posing as the Avengers' butler Edwin Jarvis) flees with the child of hero Jessica Jones and Luke Cage. This Skrull is then killed by Bullseye shortly after returning the child. Norman Osborn is placed in charge of S.H.I.E.L.D's replacement, H.A.M.M.E.R., and forms a secret group consisting of himself, Emma Frost, Namor, Doctor Doom, The Hood and Loki which commences the Dark Reign storyline.
Issue #1 was not very well received despite its strong introduction to the story, good pacing, and "slick" art style although some concerns were raised over Bendis' dialogue. Sales estimates suggested that around 250,200 copies were sold, more than twice as much as the second highest seller. The Secret Invasion: The Infiltration collected volume also topped the trade paperback chart, with an estimated 7,247 sales. The second issue kept the top slot, with estimated sales dropping to 200,344.
The following issues were released with the The Infiltration banner prior to the launch of the Secret Invasion series:Avengers: The Initiative Annual #1
Captain Marvel vol. 6, #3-5
The Mighty Avengers #7
Ms. Marvel vol. 2, #25-27
The New Avengers #38-39
The New Avengers: Illuminati #5
The following issues tie-in to the Secret Invasion mini-series:
The stories are collected in volumes:
In this reality, Earth surrendered to the Skrulls.
An issue of What If revolves around the Secret Invasion with two stories. The first story asks what would happen if the Skrulls won the Secret Invasion and eliminated poverty, war, famine, crime, and freedom. Here, the Skrulls are celebrating their anniversary of taking over Earth. Some humans have been converted into Skrulls. The Skrulls' problems is that the Avengers Alliance of Freedom (led by Captain America II and consisting of Black Panther, Blue Marvel, Human Torch, a heavily alcoholic Iron Man, Khn'nr, Ms. Marvel, Night Thrasher II, Spider-Man, Spider-Woman II, Storm, Thing, Thor, and Wolverine) are considered terrorists to the rest of the world. The Skrull's broadcast is interrupted by a pirate footage of Captain America stating that Earth is really under occupation. Queen Veranke's consort Norman Osborn tells her that it would be best to crush the Avengers Alliance of Freedom in Wakanda where they are currently hiding. Wolverine has brought one last remaining sample of the modified Legacy Virus to use against the Skrulls. He is the only survivor of the X-Men who were wiped out in San Francisco. Veranke appears before the United Nations getting an approval to invade Wakanda and take down the Avengers Alliance of Freedom. As soon as the virus was ready, the Skrull forces attack Wakanda. The Avengers leap into action to repel them. In the midst of the fighting, the cannon meant to release the vaccine is destroyed, so Thor uses his powers to spread across the globe. But instead of doing what was expected, every Skrull and converted humans perishes. The culprit is in fact Norman Osborn posing as Iron Man. He explains that this was all an elaborate ruse to get what he wants. Due to Iron Man's alcoholism, Spider-Man helped him infiltrate Wakanda to help them but he did not expect that Norman Osborn would cross the line. Now, he can only lament what he has done. Norman Osborn admits that he did create a cure for the virus, so that he could survive and get back at the Skrulls for using him. In rage, Captain America beheads Norman Osborn with his shield. The Avengers surrender to the UN forces sent to arrest them. Meanwhile, far up on the Moon, Uatu can only lament how this alternate Earth turned out.
The second story asks what would happen if the Secret Invasion remained secret. Norman Osborn is shown wondering what would happen if he was in charge of national security. Already on this Earth, Captain America has been pardoned for his role in the Civil War and is seen shaking hands with the Red Skull. Hours later, Norman Osborn and the Thunderbolts are dispatched to investigate a situation in the Savage Land. They infiltrate a mysterious structure, discovering a vault full of duplicates of superhumans from outside. The Thunderbolts attempt to fight through, only for they all to be massacred and Norman Osborn captured. He is brought before Veranke/Spider-Woman, who talked to him as if she knew him. She tells him a little story about how a priest stood up to her and told her that she would die by the hands of Norman Osborn himself. Therefore, the Skrulls had to integrate themselves into human society and eventually fade away. She claims that the prophet became Osborn himself. Though Norman Osborn tries to deny it, Veranke insists that he is and asks that he kiss her true face. Instead, Norman Osborn commits suicide reverting him to his Skrull form.The plot of the Secret Invasion storyline was adapted in the animated series The Avengers: Earth's Mightiest Heroes. A newspaper seen at the beginning of the episode "Masters of Evil" includes a headline for a Baxter Building tenant's recollections of becoming replaced by an alien. Also in the episode "The Kang Dynasty", Kang the Conqueror references to both the Civil War and the Secret Invasion by saying: "Captain America's betrayal is just the beginning... The worst is yet to come." Later, towards the end of episode "Widow's Sting", the captured Madame Hydra is revealed to be a Skrull in disguise. At the end of the episode "A Day Unlike Any Other", after the Avengers return from their battle with Loki, Captain America is attacked and replaced by a Skrull who goes on to say "The infiltration has begun" as the Skrull takes Captain America's place. In the season two premiere episode, "The Private War of Doctor Doom", Invisible Woman of the Fantastic Four was also revealed to be a Skrull. However, as of "Welcome to the Kree Empire", only Doctor Doom and Nick Fury seem aware of the infiltration. In "Who Do You Trust?", it is shown that Veranke is posing as Mockingbird. In the episode "Infiltration", the Skrull Invasion begins and Ms. Marvel is tricked by Skrull Avengers to help attack Wakanda and the Black Panther but the Skrull Avengers are later defeated when Hawkeye and the Wasp show up. Veranke also installs a virus in Iron Man's armor. In the episode "Secret Invasion", Nick Fury saves Iron Man, Captain America returns to Earth (along with the real heroes and villains who had been revealed to be replaced before), and Thor defeats the Super-Skrulls and destroys their backup plan.
Ubisoft and Marvel Entertainment stated Marvel Avengers: Battle for Earth was influenced by the Secret Invasion.
Secret Invasion is used as the basis for Chapter 10 in the plot of the game Marvel Heroes.
Marvel HeroClix released a "Secret Invasion"-themed set based on the storyline. The set included Captain Marvel, Dum-Dum Dugan, Yellowjacket, Elektra, Ms. Marvel, Jarvis, and many more. Veranke (as Spider-Woman) and Lyja (as the Invisible Woman) were released as chase figures in their Skrull-only personality.