Secret Invasion was Marvel’s major crossover event in the summer of 2008, which revolved around the infiltration off Earth’s super-human community by genetically-altered Super Skulls similar to Kl’rt. Earth is viewed as prime territory by many alien cultures and due to the large number of super-humans, all invasion attempts were thwarted and the Skrulls still view Earth as rightfully theirs. After the Kree/Skrull War when the Illuminati traveled to the Skrull throne planet to inform them not to involve Earth in their struggles anymore, the group was captured and experimented on before managing to escape. Tarnax IV was destroyed by Galactus and in the Annihilation Wave, much of the Skrull Empire was decimated, destroyed or overrun by Annihilus so the Skrulls began slowly infiltrating planet Earth and replaced various super-humans since before House of M, beginning with Spider-Woman, Hank Pym, Black Bolt, Elektra, and other various heroes. After Civil War, the Skrulls intended on implanting a Skrull in each team in the 50-State Initiative and Lyja was recruited back into the Skrull ranks to take out the Baxter Building. Dum Dum Dugan also met with de Fontaine around Captain America’s death and asked Dugan about Nick Fury’s whereabouts, but Dugan denied any knowledge.
Dugan was then stabbed with claws similar to Wolverine’s, while revealing to be a Skrull and the Skrull assumed Dugan’s form, leaving him to die. After the events of Secret War, Nick Fury went into hiding and learned Valentina Allegra de Fontaine planned to kill Fury so he killed her first and she reverted to her true Skrull form. Fury then realized an invasion was in the works so he recruited Spider-Woman to become a mole inside HYDRA and S.H.I.E.L.D. while secretly reporting to him. Meanwhile, Fury assembled a new team he believed to not have been targets of the Skrulls and in the Savage Land, the Skrulls planted a fake S.H.I.E.L.D. team that eventually engaged the Avengers, but escaped. Once Elektra was discovered it was too late because the Skrulls had already crippled Earth’s planetary defenses, the mutant population was drastically cut, super-humans were registered, on the run, killed or replace. Every team had already been infiltrated by the Skrulls and Earth was ready for the taking. Sometime after the Superhuman Registration Act (SRA), a battle broke out between the New Avengers and the Hand over the fate of Echo where she was freed from the Hand’s influence and Elektra was stabbed, to be revealed as a Skrull moments after.
Tensions began to rise amongst the New Avengers and Spider-Woman suggested they had the corpse over to Iron Man, but Luke Cage refused because he believed Stark was also a Skrull. Eventually, Spider-Woman incapacitated Wolverine and brought the corpse to Iron Man and informed him what happened in Japan. Stark did agree with Wolverine’s opinion about the beginning of the discovered invasion and convince Jessica to join the Might Avengers even though she refused to register under the SRA while Stark also believed one of his teammates was possibly a Skrull sent to kill him. Stark realized the Skrull invasion was due to the Illuminati’s attack years prior so he reassembled the group since splintering before Civil War and they debated over whether or not the invasion has taken place. The group was then brought off guard when Black Bolt voiced his opinion and it was revealed he was a Skrull as well, fighting the others over the corpse and showing himself to have not only the powers of Black Bolt, but also the combined powers of all the Illuminati members. Namor managed to kill the imposter and the Illuminati were then attacked by two more Skrulls, but they were both killed by Iron Man after he detonated a small nuclear bomb with his armor and the group went their separate ways after feeling no one was to be trusted.
Captain Marvel returned and fought with Cobalt Man and Cyclone before being confronted by a group of Skrulls posing as Kree soldiers who attempted to kill him, but were quickly defeated with Iron Man’s help. Mar-Vell then went to confront Ms. Marvel over her identity and went to interrogate Cobalt Man afterward to revealed to be a Skrull himself and mentioned Mar-Vell isn’t who he thinks he is. Meanwhile, Iron Man becomes suspicious of Mar-Vell’s true identity and sends men to Titan to investigate his grave and its discovered Captain Marvel is in fact a Skrull sleeper agent who was created to pose as Mar-Vell, but he still decided to fight against the invasion. Later, Iron Man calls in Reed Richards and Hank Pym to examine the Elektra-Skrull while a meeting between various world security agencies was held at the Peak where it’s discovered a Skrull ship has crashed in the Savage Land so Stark is called in. Stark then orders the Avengers to assemble, but Spider-Woman is the only available member and she contacted the Secret Avengers regarding the ship. The two teams meet up in the Savage Land and as Luke Cage pries the ship open, Dugan sets off an explosion which destroys S.W.O.R.D. headquarters while Jarvis uploads a virus in the Stark computer mainframe which causes Stark’s armor to malfunction and disable him.
Danvers calls the Helicarrier but there was no response since Maria Hill ordered an evacuation and the Raft loses power which frees every villain held there, and Noh-Varr also flees from the Cube. Meanwhile at the Baxter Building, a Skrull impersonates Susan Storm and opens a gateway to the Negative Zone, creating a massive vacuum, while in the Savage Land, Stark slips into a seizure as the Skrull ship opens revealing a roster of various heroes. Back at the lab, Reed discovers how the Skrulls became undetectable and Pym pulls a laser to shoot Reed and destabilize him, then transforming into a Skrull himself. Back in the Savage Land, a large group of heroes begin fighting and in the ensuing battle, Spider-Man and Hawkeye from the ship, are both killed and revert to Skrulls while Mockingbird is revealed to be the real Bobbie, also stating Captain America may be the real Cap as well. Spider-Woman disappears into the jungle while Danvers heads back to the States and Iron Man begins building a new suit and in Manhattan, the first wave of Super Skrull shock troops arrive and an attack on Britain begins shortly after.
In the Savage Land, Spider-Man confronts Ka-Zar and Shanna, believing them to be Skrulls, but they are attacked by Captain America who is later killed by Shanna after being revealed as a Skrull. In Times Square, the Young Avengers attempted battling the invading forces and the Camp Hammond Staff arrive along with its trainees, but failed to change the tide until Nick Fury arrives with his new Howling Commandos. After incapacitating Echo, Spider-Woman is revealed to be the Skrull Queen while Reed is revealed to be held by Skrull forces in Earth’s orbit and in Manhattan, Nick Fury helps turn the tide of the battle, but make a retreat after rescuing the injured heroes and plan their next move. The Hood also decides to take his new empire of criminals and battle the Skrulls while Jarvis attempts to get Hill to surrender, but she refuses. Meanwhile in the Savage Land, the Skrull Queen attempts to persuade Tony he is a Skrull sleeper agent, but Black Widow intervenes until she’s attacked by Skrulls in order to give the Skrull Queen time to escape. As the Skrulls settle in Portland, Oregon, Nick Fury and the Initiative cadets, Howling Commandos and Young Avengers arrive at his new command post while in space; Brand infiltrates the Skrull ship holding Reed captive and frees him.
Captain Marvel then arrives and destroy a large portion of the Skrull fleet and Brand takes the ship they’re on to the Savage Land while on the Helicarrier, Hill reveals herself to be a Life Model Decoy (LMD) which is killed and the real Hill self-destructs the Helicarrier. While the group in the Savage Land accuses each other of being Skrulls, Reed fires into the center of the crowd which reveals the real Skrulls and a battle begins where the invaders are then easily defeated. The invasion also reached San Francisco but the Skrulls failed to realize the X-Men were still active so they launched their nearby Super Skrulls from an orbiting ship. In Wakanda, Black Panther successfully fought off the invading Skrulls to his kingdom and sent the entire ship loaded with corpses of their invasion force to the Skrull home world while in the Negative Zone, Human Torch, Thing, Franklin, Valerie rebuild the portal and return to New York City to help with repel the invasion. The Thunderbolts then launch a counterattack on the invasion force in Washington D.C. while Noh-Varr discovers a crashed Skrull ship and discovered Captain Marvel who begs Noh-Varr to stop the invasion.
Queen Veranke arrives at Camp Hammond after the Skrulls have taken it over, the Avengers head to New York while Thor and the new Captain America arrive to help in the war against the Super Skrulls. The Skrulls quickly move to take Nova out of the fight before he returns but Kl’rt aids his former ally during Annihilation and they dispatch the group tasked to stop Rider. Back in New York, Jessica Jones and Noh-Varr arrive to take Tony’s place since he was still disabled and Clint Barton used Kate Bishop’s arrows to slay several Super Skrulls and also hits a clear shot on Veranke while the Initiative members fought their Skrull opponents and the battle heads to Camp Hammond. When Veranke was revealed to still be alive, Norman Osborn arrives to blow her head off and the remaining heroes take out the remaining Skrull armada forces while Stark finds the ship containing the heroes and humans that had been replaced. Iron Man rejoined Thor and Bucky only to discover deep-seeded resentment from previous conflicts and the invasion was solely blamed on Stark so the President ordered S.H.I.E.L.D. to shut down to be replaced by H.A.M.M.E.R. and the formation of the Dark Illuminati.