Synopsis
In Thunderbolts Mountain Captain Marvel has just defeated the Thunderbolts (#2) but hasn't killed them. Now Norman Osborn psychoanalyses him. Norman has deduced that Marvel is a Skrull fake who was programmed to initially believe his Kree identity. Now his 2 natures are at war - Osborn understands this only too well. CM heads up and away. Osborn gets the team organised for war.
In Nick Fury's secret base we find some of the Initiative trainees and Young Avengers after Fury's new Howling Commandos rescued them from Skrulls in Times Square last issue. (Stature has a reunion with her YA pals. Vision seems OK-ish after his blasting in #2.) Daisy Johnson finds that all communications are down world-wide.
Until multiple broadcasts by the images of famous people and superbeings tell the humans that they are now part of the Skrull empire. The Skrulls wish us no harm if we cooperate - they are here to save Earthmen from their own follies. The final message is that the Skrull god loves us.
Abigail Brand has broken into a Skrull warship in space, but she's been discovered. Her time in SWORD has taught her alien languages including Skrull. She bluffs her way into getting hold of a gun and then starts shooting her way through the ship until she gets to where Mr Fantastic is being held. She opens all the airlocks and ejects the remaining Skrulls into space.
Then she frees Reed Richards. (The Skrulls kept him alive because they needed his brain for something.) He quickly discovers that StarkTech has been hit by a Skrull virus (#1) (causing the worldwide comms failure amongst other things) and the top floors of the Baxter Building are gone (#1 also). Then he hatches a plan.
Maria Hill is on a SHIELD helicarrier ditched in the Bermuda Triangle (#2) surounded by SHIELD Agents who turned out to be Skrulls. Skrull-Jarvis has just asked for the surrender of the Earth (#3-4). But 'Maria Hill' explains that she's actually an LMD, on the recommendation of Nick Fury (Mighty Avengers #12). The real Hill starts shooting Skrulls then leaves by jetpack after initiating the helicarrier's self-destruct.
Meanwhile the Brand/Richards Skrull ship is under attack from others who have noticed the ejected crew. Until those ships in turn are attacked by Captain Marvel. Reed gets Abigail to fly the ship while he gets on with his plan. He wants her to head to New York to save his family, but she insists on a diversion 1st.
In the Savage Land Tony Stark is sick (literally). The Skrull virus not only crippled his armour but it attacked the Extremis in his body. (And Spider-Woman (Skrull Queen Veranke) tried to persuade him he was a Skrull last issue.) Black Widow and Wolverine are with him. They are joined by Ka-Zar, Shanna, Spider-Man and Zabu (from New Avengers #43), and then by several other characters. Everybody suspects everybody else might be a Skrull. Except Ronin (Clint Barton) who is sure that the Mockingbird who came off the Skrull ship (#1) really is his ex-wife Bobbi Morse.
White Queen from the Skrull ship arrives and claims her mental powers tell her exactly who's who. And Spider-Man for 1 is a Skrull. The arguing continues until Thor from the ship invokes the power of his hammer Mjolnir. And a 'thunderbolt' strikes the ground in front of him.
But it's not a thunderbolt, it's a blast from a weapon wielded by Mr Fantastic. And suddenly all the fakes, including Thor and White Queen, are revealed as Skrulls. (So that's what he was working on.) But they still believe they are human.
Bobbi is a Skrull, and Clint grabs a gun and shoots her in anguish. Reed Richards faces his 'wife' Sue. All the Skrulls are killed.
Spider-Woman isn't there, but Black Widow says she's a Skrull. It's confirmed by Echo who SW attacked in #3 (but who obviously didn't die).
Abigail Brand joins them and wants to fly them to New York. Ka-Zar elects to go with them. Shanna stays to mop up any remaining Skrulls. Distraught Ronin swears vengeance on the whole Skrull race.