The Skrull are invading Earth. Key figures within the Marvel Universe may have been replaced by Skrull sleeper agents. A possible Skrull invasion is on the horizon, whose seeds were planted during the Kree/Skrull war. The question is who do you trust?
The Secret Avengers remain in hiding after the conclusion of the Civil War. The current roster consists of Doctor Strange, Luke Cage, Wolverine, Spider-Woman, Iron Fist, and Spider-Man. Hawkeye, revived by the Scarlet Witch during the House of M, had approached the group wanting to join. Cage was skeptical of his alive-again teammate, but decided to allow him to join. When the team heard that Ronin was captured by The Hand under the rule of Elektra, the New Avengers flew to Japan to rescue her. Maya had been in Japan keeping tabs on Elektra and the hand as well as the Silver Samurai, hoping to try to solve the conflicts between the Hand and the Clan Yashida. Maya was killed, and resurrected by the Hand (as is their normal routine) with the intention of making her an assassin.
When the Secret Avengers reached Japan they engaged in a fight with Elektra and the Hand. Brainwashed by the Hand, Maya initially fought on the side of the Hand, resulting in Doctor Strange getting stabbed. At the end of the battle Maya turned on the hand, stabbing Elektra through the stomach. As Elektra died her features shifted into that of a Skrull.
The team takes the body back to the United States with them. The flight back is ominous, each of them examining the reasons behind the appearance of this Skrull, and its intention (the intentions of the Skrulls are typically not good). Serious questions begin to be raised. Who among the Earth's population is actually a Skrull? Who among their very ranks could be a Skrull? Is this an isolated incident, or is there something more sinister at work? The skills and magic of the Hand, the powerful magics of Doctor Strange, Spider-Man's Spidey Sense, and even Wolverine's enhanced senses were all unable to detect that this Skrull was not actually Elektra. Spider-Woman suggests that this runs even deeper and that the Skrulls may have orchestrated events which have recently damaged the relationship and credibility within the Earth's Superhero community, specifically the events of the Civil War may have been triggered by the Skrulls. Spider-Woman wonders if Iron Man could have been replaced by a Skrull, explaining his behavior during the Civil War. She expresses the desire to her teammates to take the Skrull body directly to Iron Man to determine by his reaction if he is a Skrull or not.
Other members of the team do not like this plan, but they have little time to debate. For unknown reasons, while flying back over the States their plane begins to lose altitude. Knowing that she can fly, Wolverine throws Spider-Woman out of the plane to attempt to balance the load. The plane goes down and crashes. Spider-Woman tries to get to the Skrull body to take it to Stark, but Wolverine cuts her off. She knocks him out with a powerful venom blast, and leaves with the Skrull corpse for Stark Tower.
Spider-Woman presents the Skrull body to Tony Stark, who wishes to keep it secret for the time. He arranges for another meeting with the Illuminati, a powerful group of superheroes that had clandestinely steered major past events within the Marvel Universe. Not only had the heroes of Earth come into battle on several occasions with the Skrulls, the Illuminati had as well. They had initially formed after the Kree-Skrull War, and had threatened the Skrulls that any more attacks would start a war. The members were even taken prisoner by the Skrulls and studied individually. They were able to escape back to Earth.
Iron Man brought the Skrull body to the Illuminati meeting. Black Bolt, Iron Man, Doctor Strange, Namor, Mr. Fantastic, and Professor X were all present. Along with the a fore mentioned techniques and powers that the Skrull were able to evade, Iron Man also noted that its Skrull origin was completely undetectable to his own technology. He also notes to the group that this infiltration may have been a result of what they had done to the Skrull Empire when they had initially formed. Before they could decide what to do Black Bolt reveals to the others that he was a Skrull and launches an attack. The Skrull Black Bolt uses Black Bolt's power against Namor and unleashes a powerful scream. Namor is able to kill the Skrull, but before the team can recover two more arrive. One seemingly has the powers of the X-Men's Colossus while the other is a copy of Thor. Doctor Strange is able to teleport the team to safety, and Iron Man blows up the remaining two Skrulls. Professor Xavier identified during the battle that the Skrull Black Bolt was also able undetected by Professor Xavier's telepathy. The team departs once again, not knowing who they can trust.
Tony Stark has to figure out how to handle this secret invasion. He summons Medusa and Crystal and talks to them with the Black Bolt Skrull corpse in between. Medusa demands an explanation, Tony not knowing much about himself all he tells them is that an invasion is rising and problems will arrive. Medusa then takes the body and leaves to the moon.
Stark arranges for Mr. Fantastic and Hank Pym to study the Skrull-Elektra body at a secret Stark Laboratory. He doesn't know who he can trust, even the Richards or Pym, and he must discover why the Skrulls are completely undetectable to psychics, technology, magic, and enhanced senses, and any other ability. Hank and Reed begin work to uncover the Skrull secrets.
Meanwhile on the SWORD satellite headquarters known as The Peak, commanding officer Dum Dum Dugan and recently arrived Agent Abigail Brand witness an unidentified Skrull transport spacecraft entering Earth's atmosphere and about to crash-land in the Savage Land. They contact Stark, who leaves Richards and Pym to work on the Skrull body to determine how they are both completely undetectable and able to copy the powers of Earth's superheroes. Stark flies off to locate the other members of the Mighty Avengers to investigate the crash site.
Susan Richards had been in Vancouver in a conference. There she was surprised by her husband Reed. She later discovered that he was a Skrull and he was there to capture the Invisible Woman using powers like her.
Medusa arrives to the Inhumans with the Skrull corpse and suggests that the Inhumans take care of this matter. The Inhuman king raises the question of who can be trusted. Crystal then doubts if maybe Iron man was right about a war coming and problems arising.
While Stark is attempting to arrange for the Mighty Avengers to all meet for the flight, Spider-Woman contacts the Secret Avengers to let them know that they can get there before Stark can. Cage calls Cloak for a favor, and has him teleport the group to the Avengers tower to take the Avengers Quinjet. Only Black Widow was there at the time, and the team is easily able to take her down. With a mode of transportation, they fly for the Savage Land.
Once in the Savage Land, the Quinjet is damaged by a dinosaur, and crash lands in the top of a tree. The group exits and notices that the building where they had their first battle as the Avengers was destroyed. Next they come upon the crash-landed Skrull craft. Before they get a chance to open it, Iron Man and the Mighty Avengers arrive. In direct defiance to Stark's wishes, Cage rips the door off of the Skrull craft. A light on the craft turns from red to green, and Skrull sleeper agents around the world are activated.
On The Peak, Dugan's eyes glow green and he says "He loves you..." before he detonates the space station. From the Avengers Tower, Jarvis uploads a Skrull Virus into Stark's armor causing it to go haywire, and also says "He loves you...". Using Stark's Extremis link to the world's satellite system, the virus takes control of the SHIELD Helicarrier which begins to go down. Systems in Stark enterprises plants, Stark satellites orbiting the planet, and the maximum security prison for superhumans known as The Raft are each compromised. Prisoners within The Raft are able to escape once again. Another maximum security penitentiary known as the The Cube is also under siege by its inmates. There is an explosion at Thunderbolts Mountain as someone who appears to be Captain Marvel arrives. At the public headquarters of the Fantastic Four, a Skrull version of the Invisible Woman sets off a The Negative Zone gateway which sucks half of the tower into the Negative Zone.
Back in the savage land, individuals purporting to be several of Earth's superheroes emerge from the Skrull ship. These heroes were: Spider-Man, Luke Cage, Phoenix, Emma Frost, Beast, Mockingbird, Captain America, Hawkeye, Wolverine, Thor, Iron Man, Scarlet Witch, Ms. Marvel, Invisible Woman and Vision. Wanting to know who the members of the two teams of Avengers are. Back at the Stark Industries secret location, Reed Richards finally discovers the way that the Skrulls were able to make themselves undetectable. He is about to share this information with Hank Pym who takes out a Skrull weapon and fires at Richards, causing him to lose control of his elastic powers and sending his body all over the room. This Pym impostor changes into a Skrull and tells Richards that "He even loves you".
While in the Savage Land the heroes that came out of the ship and the Avengers (and Secret Avengers) face each other. Ares makes note that this is only to distract them but they still face off in an epic battle. While they all fight the Avenger Ms. Marvel took the injured Tony out of the battle field. The Sentry tries to talk to Vision but the Vision transforms into his "evil self" and blames him for these events. Ronin then takes Hawkeye's bow and arrow and shoots Beast, Emma Frost and tries to shoot Captain America but fails. Cap was able to shield his attack making Hawkeye doubt if he really is Steve Rogers. Then a T-Rex arrives into the scene and kills two of the Spider-Man and Hawkeye from the Skrull ship. Carol takes Shell Head to the base where the New Avengers first joined forces and Iron Man then said he was going to make another Iron Man suit from the material he had around and sent Danvers to the mainland. Luke Cage and Wolverine see the dead Spidey and conclude that all of the heroes from the ship are Skrulls. The they see Mockingbird crying over the death of the Hawkeye Skrull. She claimed to be the real thing and before Wolverine can hurt her Ronin stops him. He asks her what happened on October 12th. She answers: "I-I had a miscarriage. We didn't tell anyone. Me and my husband. We figured his birthday would have been October 12th". This proves to Clint that she is in fact the real deal. They kiss and Ronin tell Wolverine to trust him. Mockingbird mentions that she thinks that Captain America is also the real deal since he's the one who brought them back to earth.
Back in Manhattan the Young Avengers watch as the Baxter Building eats itself up. Then they spot a Skrull ship that sents down many Skrulls that have the powers of heroes and villans including armor that looks like Iron Man's.
In the Negative Zone part of the Baxter Building appeared. Johnny, Ben, Valeria and Franklin and Sue were all there. Creatures from the N-Zone started attacking where the Thing, Franklin, and Valeria were at. Ben kept them safe from the "big bugs" and took them to a cupboard and told Franklin to take care of his sister. In Reed's lab Johnny and Sue debated on who was she. Johnny asked her what her favorite movie was and she got it wrong he knew something was wrong. Sue then turned into a Skrull and not just any Skrull but Johnny's ex, Lyja.
Skrull Jarvis appears on waters where the Hellicarrier fell to tell Maria Hill to surrender. Captain Marvel keeps fighting the Thunderbolts and Osborn tries to reason with him. The Young Avengers are now in the fight between all the Skrulls arriving in Manhattan while the Runaways are just arriving to the scene. An epic battle happens between the The Initiative and the Skrull armada. The Initiative being led by Yellowjacket. Back in the Savage Land Tony is trying to create a new suit then Spider-Woman appears into the place where Tony's at after fighting and winning a fight with Echo. She thanks Tony Stark for helping the Skrull Invasion be a success. She kisses him and tells Iron Man that he doesn't remember it but he is trained not to remember him being a Kr'Ali Skrull Soldier and the love of the Queen. Everything from the Civil War and the Invasion was planned.
In the Negative Zone Lyja and Johnny fight against each other into the N-Zone. Lyja gets caught by an N-Zone "squid" and Human Torch helps her. He kisses her reliving old times. Franklin and Val get out of their hiding place and go get a machine that their dad made for them for defense purposes. Ben keeps fighting N-Zone bugs and Franklin and Val help to fight. Johnny and Lyja fuse power together to free her making Lyja pass out. Back at the Baxter Building the four decide what to do then Franklin suggests that they get help from a prisoner from the N-Zone prison.
In Times Square the battle keeps going and during the fight Skrull soldiers destroy Vision while claiming that they wouldn't win. Then a Skrull was killed by Nick Fury.
The Howling Commandos and Nick Fury started killing every Skrull that could be see while back at the Savage Land Iron Man is trying to recover from the news of "Spider-Woman". Black Widow is listening to the whole conversation then Beast and Phoenix arrive and Widow kills them revealing them as Skrulls. Spider-Woman hears this and flees. Widow then tries to help Iron Man by giving him a shot of adrenaline. Wolverine arrives and Black Widow shoots him until she made sure it was him. She sent Logan to kill the Skrull queen while she helped Tony up. He then agrees that even if he was a Skrull he wants to kill the Skrulls.
The Fantastic Four (Human Torch, Thing, Franklyn and Valeria) head to the N-Zone prison. On their way Val falls off the Fantasticar. Lyja then arrives and saves her claiming that she was there to help. Johnny stay back with Lyja while the rest go in to find the Thinkerer. Lyja explains that she was sent to kill them all but having her feelings involved she decided on taking them to the N-Zone. The Thing bust out Thinkerer after an agreement. He fixes the baxter and finds a way to get back. Lyja decides to stay back and the rest arrive to see the city destroyed.
Back in Times Square Fury keeps fighting and Ms. Marvel arrives to the scene to try and help. When the fight's over Fury shoots Ms. Marvel and they keep on fighting. Then a bolt of lightning shoot down from the sky, Thor arrives, and at the same time Captain America (Bucky) arrives.
In Asgard Thor is trying to deliver a baby when Beta Ray Bill arrived in crash land form. He told Thor that he was taken captive by Skrulls and then was sent there while them keeping his hammer. Loki (Woman form) started then spreading mischief by questioning if that was Beta Ray Bill. Asgardians started to question if he was a Skrull. Thor proved his worth by letting him use Mjolnir. Then he went back to delivering the baby when Skrull ships arrived.
In San Fransisco Skrulls started their invasion but were surprised by the attack of the X-Men. During the whole commotion the Skrulls had to improvise on how to react with the X-Men and then attack back. All X-Men split up into teams around San Francisco and defended the people. The Skrulls had then used a mechanism that blocks off Psychic powers hurting Emma Frost. Nightcrawler then found an ancient Skrull bible that was held by a Skrull priest but he was then pursued by super powered Skrulls.
Medusa wonders at night of what could have happened to her husband and if he´s still alive then she sees a what seems to be Black Bolt at the window. She heads out and to her surprise a Skrull with some of the Inhumans powers takes her by the neck and hangs her out of the window. Someplace else a Skrull smirks at how they will use Black Bolts power in the war and take advantage of it.
Jackpot after getting bad publicity for a mistake she had done the night before she goes to the Daily Bugle for a retraction there Spider-Man who turned out to be a Skrull with the powers of the Sinister Six.
On the Skrull ship Reed is being tortured and Agent Brand with her ability to speak Skrull frees him. Captain Marvel helps them both free themselves from a Skrull armada. Reed using a machine that reveals who are really Skrulls, stops a dispute between the heroes from the ship and the rest of the Avengers. He reveals all the heroes from the ship are actually Skrulls including Mockingbird. The Skrull impersonating Sue Richards was surprised to know that Reed had children and most of the Skrulls were surprised to see they were actually Skrulls. Clint Barton declared to kill every Skrull after what had happened to him.
The Skrull queen then arrives at New York pleased with the events. Hank Pym or at least the Skrull leads the queen to see how the advances are made.
At the same time the Avengers that were arriving from the Savage Land are arriving to New York and see the city in full blown invasion. Captain America and Thor face to face wonder what has happened around them and at the same time Iron Man then fixes his armor. The Thunderbolts then join the Avengers, Thor and Captain America. Nick Fury and the Young Avengers plus the Commandos join in the fight. The Skrull queen faces these group and tells them again that "he" loves them all.
Spider-Man: Uh, who is he?
Nick Fury: Yeah? Well my god's got a hammer!
Iron Man: Right... Avengers.... ASSEMBLE!!!!!!!!
Then a massive war between the heroes, villians, and Skrulls have a mass out war in Central Park. The heroes attack the Skrulls constantly. Nick Fury and Norman Osborn remark that the other should be in jail, Captain America and Natasha Romanoff go in for an offensive attack, and Iron Man is holding his armor with rubber bands. Wasp goes in to take out Skrull Hank Pym, but he reverts to his Skrull self and grows to his 'giant' size only to be taken out by Stature. Wolverine attempts to attack Veranke, only to have his skin burn off by her venom blasts. Then Uatu, the Watcher shows up. Jessica Jones watching the events unfold on tv, leaves her child in the care of 'Jarvis-The-Skrull'. Noh-Varr then enters the war claiming earth in the name of Mar-Vell.
Hawkeye is injured in the battle and the Vision takes her to safety while Ronin picks up his old bow and arrow. He takes out three Super-Skrulls and then shoots an arrow through Veranke's neck, exiting through her cheek. Although it seems she's dead, she's not. However Crito-Noll activates the formula he gave the Wasp several days ago and she begins to grow large. Skrull Jarvis then states that it doesn't matter if the Skrulls live or die just as long as 'God's' will is done. Janet begins to emit purple energy and entraps the heroes, villains and Skrulls in the energy.
Janet Pym is now the massive weapon that no one will survive. Thor pops in and makes her disappear just while dying. The Skrull Queen is still alive and as she is about to be killed by Wolverine, Norman Osborn gets the kill shot. The shot would become "the shot heard 'round the world' due to all news networks covering the event. Iron Man and Thor go into space and take down a Skrull ship which uncovers all of the replaced people by Skrulls. Including Spider-Woman, Invisible Woman, Yellowjacket and Jarvis which makes Jessica Jones realize her baby is with a Skrull. When she goes back she can't find the baby nor the Skrull. Nick Fury leaves in a hurry when Dugan wanted to say hi.
The president, after this, takes down SHIELD and makes Norman Osborn leader of the Thunderbolts initiative leaving all of SHIELD's old responsibilities to him. Stark Enterprises are no longer a resource for weapons and Tony and Maria Hill are now unemployed.
Then Norman Osborn heads to the basement of Avengers Tower where he finds the Hood, Loki, Dr. Doom, Namor and Emma Frost and tells them: "Okay. It's a new day. So listen carefully... This is how it's going to be..."
Beginning the Dark Reign.
List of those confirmed to have been replaced by Skrulls:
- Black Bolt - confirmed in New Avengers: Illuminati #5 - Killed by Namor
- Elektra - confirmed in New Avengers #31 - Killed by Echo
- Revolutionary - Confirmed in Avengers: The Initiative Annual #1
- Dum Dum Dugan - confirmed in Secret Invasion Prologue
- Contessa Valentina Allegra de Fontaine - confirmed in Secret Invasion Prologue - Killed by Nick Fury
- Hank Pym (YellowJacket) - confirmed in Secret Invasion #1
- Edwin Jarvis- confirmed in Secret Invasion #2
- Cobalt Man - Captain Marvel #3
- Cyclone - Captain Marvel #4
- Captain Marvel - confirmed in Captain Marvel #5 of 5
- Spider-Woman - New Avengers #40
- Magnitude - Avengers: The Initiative #14
- Longshot - Revealed as a Nogor, a Skrull religious figure in X Factor #33 (The real Longshot turned up in X Factor #35)
- Brother Voodoo - Revealed as a Skrull in Black Panther #38. - Killed by Cannibal
- Sharon Ventura - Avengers: The Initiative #16 - Killed by Skrull Kill Krew
- Blacksmith - Avengers: The Initiative #16 - Killed by 3-D Man
- Ahura - Secret Invasion: Inhumans #2 - Defeated by Maximus