The story begins with Luke Cage and Jessica Jones returning home to their apartment. As they open the door,they are ambushed by a mystery assailant. Meanwhile at the Helicarrier, agents of S.H.I.E.L.D are informing Nick of all the things and disasters that are going on in the world, all in which he doesn't take seriously until he finds out about Luke Cages attack and that Cage is now in a Coma. Fury then visits Cage in the hospital who finds Danny Rand aka Iron Fist and Jessica Jones. As Jessica question's Fury's reason for being there, a flashback occurs one year before. Killer Shrike (Simon Maddicks) is in custody after having been apprehended by Iron Man and Thor. In custody, Maddicks quickly finds out that the cops are Shield agents and after interrogating him violently, Maddicks quickly agrees to tell them everything. Maddicks leads Shield to his tech benefactor. Unfortunately Maddicks benefactor who is revealed to be the Tinkerer, who catches on to Maddicks betrayal and activates a booby trap giving him enough time to escape and results in Maddicks being seriously wounded.
Later the Shield agents raid the place but discover the tech of other super villains and four old passports with different names. Fury then gets a call from Black Widow who tells Fury that she has found the Tinkerer in Latveria. Fury later meets his superiors to notify them of the conspiracy he has found. Fury tells them about tech being made for various super villains that cost a lot more then the money they get from attempting to steal. Fury then reveals that the Tinkerer has been making tech for various super villains in the U.S but is getting funding him self from Latveria making the actions of the Super villains terrorism. Fury recommendation of action is rejected by his superiors who say that the United States has a good relationship with Latveria and wish to not take action but handle things diplomatically. Shocked, Fury storms out of the room where Contessa Valentina Allegra de Fontaine asks him what is he gonna do? The story then continues to the present day as Fury looks over the body of Luke Cage and says "What have I done".
One year ago, Fury approaches Captain America at his apartment resting after a mission. Fury requests for Caps help and tells him that it's "Big". Cap offers to assemble the other avengers but Fury says he needs this one to be a secret. Meanwhile elsewhere, Daredevil returns to his office as Matt Murdock and smells Fury at his office. After recruiting Daredevil, Fury then meets Luke Cage who just busted a drug seller. Shortly after Spider-Man swings back home to find Fury sitting down with Mary Jane. Fury then tells Peter that he needs Peter Parker and not Spider-Man.
The next day Peter goes to the airport and boards a plane and finds him self sitting next to Matt Murdock. The two are trying to figure out what is going on when Wolverine causes a scene at the back of the plane due to being drunk. His obscene behavior is put to an end by Steve Rogers aka Captain America. The plane then takes off and arrives at Latveria. The heroes Fury are recruited (except for Steve Rogers who goes off with the Latverian government) are greeted at the Latverian air port by Natasha Romanov aka Black Widow and with them another teenage girl follows, they all meet where Fury reveals him self to them. He then informs the heroes of the conspiracy he has discovered and tells them that he recruited them to help him overthrow the government. The story then continues to the present day, as Fury watches Luke sadly, Captain America burst in and punches Fury yelling "Damn you for what you did to us!!!!!"
In the present day, Peter Parker is having his anniversary with Mary Jane but keeps getting visions in his head of a fight occurring in Latveria involving him and the other heroes Fury recruited fighting soldiers with tech similar to that of previous Super villains. Peter who cant sleep because of the visions goes to visit Daredevil, they meet and Peter tells him about the visions. Peter also knows that the fight hes seeing happened in Latveria but he recalls never having been there before. Daredevil tells Peter that he knows nothing about the visions, Matt then gets a call from Jessica Jones who tells Matt that Luke is in the Hospital. As Spidey and Daredevil are about to leave they are ambushed by Diamondback and Scorcher. Spidey and Daredevil make quick work of them and make their way to the hospital. Back at the hospital outside, Cap tells Fury how he was attacked outside his apartment by Hobgoblin and Lady Octopus. The two are joined by Spiderman and Daredevil. Cap explains to them that the attacks are happening because its the anniversary of their Secret
War but Spiderman and Daredevil have no idea what that means. The heroes are then attacked by an army of super villains. Meanwhile back at the Xavier Institute Wolverine is drinking quietly until he is attacked. Back at the hospital, the heroes fight the massive amount of super villains as best they can. As they are about to be beaten, the Fantastic Four arrive and back them up but not long after the super villains tech suddenly malfunction and the energy is transferred into an Android Lucia Von Bardes. The heroes attack her under Fury's orders but are unable to penetrate her force field. Cap then orders the heroes to cut the line by damaging the tech worn by the army of super villains that she is getting her energy from. The plan fails however and Lucia charges up her energy to create a large explosion.
As Lucia charges her energy she yells angrily at Fury blaming him for everything. Before she can make her attack her mechanical heart suddenly explodes and after a backlash explosion she is defeated. The heroes pick them selves up and discover that the teenager named Daisy Johnson mentioned before one year ago had defeated her. The Black Bird arrives with Wolverine and the other X-Men. Cap demands Fury to tell them what had happened one year ago on that present day which was the "Secret War". Fury reveals that the heroes he recruited helped him attack Latveria. The heroes who had been previously recruited fought there way to Castle Von Doom to confront the Prime Minister Lucia Von Bardas. The heroes are surprised to find out that they weren't officially allowed to attack Latveria and are even more shocked as Fury orders Daisy Johnson to bring down the whole castle which she agrees.
The heroes survive the destruction of Castle Von Doom but are disgusted at what Fury had done. Back in the present day, Spider-Man asks Fury why none of them remember this in which Fury reveals he mind-wiped them so none of them would remember and Cap only got back his memories when he did his regular Shield check up. Fury justifies his actions saying that he could not allow his superiors to do nothing and believed that what he did was the right thing to do. Wolverine flies into a rage for being mind-wiped again and strikes Fury directly and continue to slashes him. Wolverine then gets taken down by Daisy Johnson who explodes Wolverines heart knowing he'll live.
Daisy then reveals to the heroes that what Wolverine sliced was a Life Model Decoy and that the real Fury had left several minutes after Lucia Von Bardas was defeated. From afar, Fury apologizes to the heroes for what he did through the LMD and says that they won't be seeing him again. The story later shifts to Daisy Johnson who is being interrogated by Maria Hill who is now the new director of Shield on the whereabouts of Nick Fury. Daisy tells her she doesn't know and is yelled at to leave. As Daisy walks on to the platform of the Helicarrier she gets a call in which she says "yes sir" leaving readers to believe that she does know the whereabouts of Nick Fury.