Secret Invasion - Plot

Plot

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 and 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 intel 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.