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 Spoilers Secret Invasion 1-5 and Tie ins

Iron Man reveals the corpse of the Elektra impostor to Hank Pym and Reed Richards (who pretends he has never seen the corpse before) and leaves the two to study the body. Then he assembles the Mighty Avengers to investigate the wreck of a Skrull spaceship in the Savage Land, unaware of the fact that the New Avengers are heading for there as well after being tipped off by Spider-Woman. As Luke Cage opens the downed ship, a chain reaction of events takes place. S.W.O.R.D.’s headquarters in space is destroyed by the Skrull now posing as Dum Dum Dugan, while in Avengers Tower, a Skrull disguised as Edwin Jarvis inserts a computer virus into Stark Tower’s mainframe that causes every computer system controlled by Iron Man to crash, including Iron Man’s armor and the S.H.I.E.L.D. Helicarrier, which is evacuated as it starts to lose power. This virus also releases super-powered prisoners from the Raft. This also occurs at the Cube as Noh-Varr leaves amid the chaos. In addition, Captain Marvel, who had gone to the Skrulls and agreed to help, attacks Thunderbolts Mountain for his own personal reasons, believing that the team was truly evil and needed to be destroyed.

A Skrull agent poses as Reed Richards and attacks Susan Storm whilst she is at a conference in Vancouver, rendering her unconscious and supposedly capturing her. Afterwards, the Skrull Lyja takes on Susan’s form and sends the Baxter Building into the Negative Zone. As Ben Grimm attempts to protect the Richards children from Negative Zone insects, Lyja attacks her former husband Johnny Storm. Each Skrull agent mouths the words “he loves you” before putting their part of the plan in to action.

The Skrull spaceship is shown to hold a large group of Marvel superheroes (Beast, Thor, Spider-Man, Phoenix, Iron Man, Wonder Man, Scarlet Witch, Invisible Woman, Captain America, Wolverine, Mockingbird, Power Man, Hawkeye, Emma Frost, Vision, Ms. Marvel and Jewel) with older appearances and costumes, speaking as if they believe themselves to be authentic. Floating in space in a stasis gel with only minutes of oxygen left, Agent Abigail Brand witnesses a massive Skrull armada heading for Earth. Elsewhere, Reed Richards conducts an autopsy on the Elektra Skrull corpse and learns how the Skrulls are avoiding detection, but is quickly shot in the face before he can share the information with others by Pym, who reveals himself to be Criti Noll and leaves Richards unable to remain solid.

Despite the urging of Ares that their confrontation is merely a distraction from the true battle, the assembled heroes from the ship and their counterparts on Earth begin fighting, both sides convinced that their opponents are the Skrulls. In the ensuing battle, the Spider-Man and Hawkeye from the ship are both killed by a native Tyrannosaurus and Clint Barton in his Ronin guise respectively, and both revert into their Skrull forms. The Mockingbird that appeared insists she is not an impostor, as she and the New Avengers’ Clint Barton make a tearful reunion after answering a question that the only the real Mockingbird could know. Mockingbird also states that the Captain America from the ship may, in fact, be the genuine article. While Spider-Woman disappears into the jungle and Earth’s Ms. Marvel heads back to the States, Earth’s Iron Man (still suffering from the Skrull virus) starts to build himself a new suit from the wreckage of a nearby lab. The Sentry faces the ship’s Vision and flies away to space filled with terror being convinced that the ship’s Vision is The Void. While all this happens, Spider-Man confronts Ka-Zar and Shanna, accusing them of being Skrulls. However, they are attacked by the ship’s Captain America. Meanwhile in Manhattan, the first wave of Super Skrull shock troops bearing the abilities of Earth’s superhumans arrive, as witnessed by the Young Avengers.

The S.H.I.E.L.D. Helicarrier has crashed in the Bermuda Triangle and all of its systems are down, due to the virus introduced by the Skrull posing as Jarvis^.When Deputy Commander Hill reaches the upper deck of the Helicarrier, she finds Jarvis, who requests S.H.I.E.L.D.’s immediate surrender. At the Thunderbolt’s headquarters in the Colorado Rockies, Captain Marvel has succeeded in defeating the Thunderbolts, but is unable to kill any of them. Realizing that their attacker will not kill them and is not who he seems to be, Norman Osborn approaches Captain Marvel and convinces him to defect and aid the humans. At Camp Hammond, Yellowjacket (who is not known to be a Skrull by anyone other than the incapacitated Mr. Fantastic) tells Gauntlet to rally the cadets as New York City is under attack.

Whilst all of this is happening, Reed Richards is revealed to being held by Skrull forces up in Earth’s orbit on the Skrull Mothership, stretched to his physical limits and surrounded by a crowd of Skrull watchers and scientists, helpless against the threats and torture. Agent Abigail Brand of S.W.O.R.D. manages to break through the exterior of another ship and make it into one of the central control rooms, seeing the images of the invasion, death, and destruction the Skrulls are making on Earth, as well as the torture of Mr. Fantastic. Discovered by the Skrulls, Brand is able to bluff her way out of execution, before going on a rampage through the Skrull vessel, killing the entire crew and rescuing Richards. The Sentry is shown up in orbit, still being tormented by the false words of the Skrull Void impostor and refusing to help.

Down in the chaotic battle in Manhattan, Nick Fury and the new Howling Commandos show promises of turning the tide; Ms. Marvel, after being heavily blasted by a group of Skrull soldiers ends up rising in the middle of Fury and his group in Times Square as they fight, shocked by the return of the ex S.H.I.E.L.D. leader. As they quickly head into the fray, Yo-Yo, the team’s mutant speedster, manages to rescue all the downed Young Avengers and Initiative cadets before further killings after Geldoff-Proton’s one. Vision II is also severely damaged but self-repairs in some way. Ms. Marvel proceeds to help, but soon after is shot by Fury, who is unconvinced she is the real Carol Danvers. After being shot back into another street, the Skrull onlookers quickly overrun her, with the Skrull Henry Pym looking down at her with a smirk on his face. Fury then calls his men to retreat so that they can plan the next move.

Meanwhile, the Skrull invasion continues across the rest of the planet, to varying degrees of success. An attempt to seize control of Earth’s magic in Britain is repelled by Captain Britain and his MI:13 teammates, while a bold strategy from the Black Panther leaves the Skrulls without technology as they attempt to seize Wakanda. Attacks against San Francisco and Attilan are met with resistance from the X-Men and Inhumans, respectively, while Thor, Beta Ray Bill and the Asgardians defend Oklahoma from the invaders. All the while, Hercules leads the God Squad into the realm of the Skrull Gods in hopes of stopping the invasion at its source.

Watching the battle via news broadcast on live television, the Hood decides that a Skrull-controlled Earth would be detrimental to business and mobilizes his army of super-villains. In the Savage Land, Spider-Woman continues to convince Tony that he is a Skrull sleeper agent named Kl’Riki Dulu, who she will praise as the greatest Skrull Warrior to ever live. The Black Widow watches the conversation, and proceeds to enter and shoot Veranke/Spider-Woman after dispatching the ship’s Beast and Phoenix as they regress to Skrulls upon death. Spider-Woman escapes and Natasha injects Tony with a dose of adrenaline to keep him going, while convincing him to keep fighting. Wolverine enters after being shot by Black Widow and being forced to confirm his true identity through the codeword (”Carrot Sticks”). The three of them conclude that Tony has to rebuild his armor quick and return to New York as soon as possible.

In New York, Nick Fury and his Commandos rescue the other superhuman defenders and move on while several civilians are saved from Skrull soldiers by Thor, who kills the Skrulls with several blasts of lightning. The incident is witnessed by the new Captain America.

The Skrulls settle in Portland, Oregon, enslaving the population. Gorilla-Man and M-11, disguised as slaves, attack the Skrulls, freeing Namora in the process. The three heroes capture the regional Skrull commander, taking only his head, bringing it to their underwater saucer where Bob Grayson and Venus are waiting. They extract military secrets from the severed head just as they are counter attacked. The unlikely team fights back, liberating Portland. They begin a brave plan to free Seattle, the rest of America, then Japan–all the while wondering if they can trust anyone but themselves.

At Thunderbolt Mountain, during a conversation with Norman Osborn, Khn’nr decides to rebel against the Skrull empire and leaves Thunderbolt Mountain to attack the Skrull armada out in space.

Nick Fury arrives with the Initiative cadets, his new Howling Commandos, and the Young Avengers at his new command post. The Vision has survived his attempted murder by the Skrulls, but remains rather disfigured/damaged. He awaits with his team for the Skrulls to announced their plans for Earth and they do. Using generated images of various leaders and famous stars including Magneto, the Pope, Barack Obama, Tom Cruise, John McCain, Simon Cowell, Eric Cartman, Tony Stark, Namor, Oprah Winfrey, Doctor Doom, Kim Jong Il, and others, the Skrulls announce that they intend on assimilating all humans into their culture and way of life, declaring Earth part of the Skrull empire. The only way for the human race to save their planet is to assimilate…

Meanwhile in space, Agent Brand infiltrates the Skrull ship holding Mister Fantastic captive. She battles the Skrulls who are experimenting on him, either killing or disabling them and freeing Richards. Frustrated, she decompresses the ship, throwing every Skrull out into space. Richards panics, threatening Brand, demanding the location of his family, believing her to be a Skrull. He reveals that the Skrulls needed him alive to assist in the invasion. Richards tests Brand to prove she is not a Skrull as the ship they have commandeered comes under attack. Out of nowhere, Captain Marvel, with a new sense of purpose, engages and destroys a large portion of the Skrull fleet. Brand then takes the ship and Richards to the the Savage Land.

Back on the S.H.I.E.L.D. Helicarrier, Maria Hill reveals to “Jarvis” and the Skrull insurgents that she is using a life model decoy as Fury had suggested to her many months ago. The Skrulls destroy the duplicate, but the true Maria Hill, on a jetpack, opens fire on the Skrulls and destroys the Helicarrier using a self-destruct sequence.

The various Avengers, Savage Land leaders, and duplicate heroes are again at an impasse. Each side declares who they are or who they believe themselves to be. The ship’s Emma Frost states she can detect who is a Skrull and who is not, accusing Spider-Man of being an impostor. The ship’s Susan Storm states she will keep everyone in place with a force field until all is settled. Abigail Brand and Reed Richards arrive as Reed fires into the center of the crowd of super heroes with an odd weapon. When tech dust and brightness recede, the Skrulls and humans are revealed, a battle ensues. Ronin discovers his Mockingbird is a Skrull, grabs one of Black Widow’s guns, and kills her in anger. The impostors (Thor, Emma Frost, Wonder Man, Ms. Marvel, Jewel, Mockingbird and Susan Storm) seem surprised and disoriented when their skin turns green, making them easier to take down by the Avengers. Ronin, angry and frustrated at the realization his wife was an impostor, declares that every last Skrull must be killed.

The invasion reaches San Francisco, new home of the X-Men. Believing the city to be virtually defenseless except for local police, they launch a small scale attack to cause enough damage to instill fear. However, their ground teams encounter unexpected superhuman resistance: each and everyone of the X-Men that are still active. The X-Men launch a counter strike, defending civilians and evacuating badly attacked buildings. The Skrulls are shocked to find the X-Men in San Francisco especially when they take over their command shuttle. As the X-Men make a successful gain, the Skrulls launch their super soldiers into the city from an orbiting ship.

Trapped in the Negative Zone, Johnny Storm, The Thing, Franklin and Valerie Richards, and Lyja turn to the prison population to rebuild the destroyed portal generator in order to return to Earth and help repel the invasion. The one they turn to is the Tinkerer. He tells the Fantastic Four that he was forcefully taken even after retiring from supervillain work, revealing that the unregistered superhumans did not receive a fair trial. The Tinkerer then refuses to help. After Franklin pleads with the man, Tinkerer complies at the child’s desire to return to his family. As Lyja stays behind, the others successfully return back to New York City which is now a battleground.

At New Asgard, Thor has rescued Beta Ray Bill, who is without his magic hammer Stormbreaker following his release from the Skrulls. Loki and the other Asgardians suspect Beta Ray Bill is a Skrull, and they plot to attack while he is recuperating. Thor intervenes by throwing his own hammer, Mjolnir, at Beta Ray Bill who catches it, one of the few beings besides Thor worthy to lift the sacred hammer. Beta Ray Bill, healed by holding Mjolnir, joins Thor in his fight against the Skrulls as some of them attack Asgard.

Delroy Garrett later encounters the Skrull Kill Krew and Delroy ends up being helpful when his goggles detect She-Thing as a Skrull

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