In London, below the hovering ship of Mikhail Rasputin, thousand of volunteers head towards the transport ships. These ships have been sent to take them to a facility on Mikhail’s ship to begin their augmentation process and become the next wave of enhanced humans in Mikhail’s army. A man named Rafe stands near a statue of a World War I soldier. Rafe talks to his wife, Marta, of how he hopes that he is not wrong and that Mikhail’s promises lead them and their son to a better life are true. Both kiss and Marta climbs down the statue to head to the transport ship with her son. On Mikhail’s ship the leaders who had greeted Mikhail are trapped in stasis chambers, awaiting their turn on the operating table and begin their augmentation process. Tony Stark is already lying on the operating table. Thanks to an accident when he was younger, Tony Stark almost died, but his genius with mechanics was able to save him. Tony wears a mechanical heart, so Mikhail believes him to be the best of the lot for accepting the augmentations. As the others watch from their glass chambers, they are able to see a mechanical syringe getting closer to Tony’s heart and slowly puncturing his skin until the syringe is in his chest.
Elsewhere on Mikhail’s ship, the Keeper watches over Empath, who is being kept alive by the wires that come from his body to the machines above. The Keeper tells him that being sensitive in today’s world does not pay. A doctor, in the shadows behind the Keeper, tells him that he must keep Empath alive so he can continue to fan the flames of insurrection in the humans below them.
Below the ship, the humans chant the name of Mikhail and also cry Unity. Not so far away in an abandoned building, the last remaining members of the Human High Council meet to discuss the growing instability of the civilians around them. The three members of the Council are Bolivar Trask, his wife Moira Mactaggert-Trask, and Thunderbolt Ross, a five star general of an American Army that no longer exists. While the three talk, in the shadows, Mikhail lurks and listens to their conversation. As Ross talks, Mikhail steps out and interrupts him, telling them that their choices are out of their hands now. As the three members stare in shock in Mikhail’s presence, Mikhail angrily tells them that if the humans cannot stand together, the mutants will destroy them, because at least mutants are committed to a common cause.
Tony contorts in pain as the syringe bursts through his mechanical heart. The resistance leaders knew that Mikhail had been experimenting on humans and that whomever they sent aboard the ship would become part of the experiment as well. So, they rewired Tony’s heart to cause a feedback throughout the ship when the syringe entered Stark’s heart. As the feedback occurs, and a temporary short-circuiting of the power supply happens, it comes at a cost of giving Stark a cardiac arrest. “We’re free,” cries one of the captured civilians as he also begins to take charge of the other civilians. He orders them to find anyone else who cannot walk and to help them escape. Von Doom escapes from his cell, as does everyone else does, and they all run to Donald Blake’s side to help him free himself. After being pulled free by Doom, Blake only takes a second to collect his thoughts before he runs to the operation table to see if he can do anything to save Stark’s life. Gwen is already there and is applying CPR, which is not working. Blake orders her to back off of him while he pulls a syringe from his pocket that is full of adrenaline. He plunges it into Stark’s heart, thankfully saving his life. As Stark raises himself off the bed the entire team is surprised to see that their plan is going just the way they had wanted it. Ben watches from the background and says out loud that “Operation: Trojan Horse” has only just begun. Tony tells Grimm that the tracking devices they had placed earlier on Grimm’s weapons is still signaling to his internal sensors, leading them straight to the Ammo Dump.
In front of the ammo dump, a few of Mikhail’s soldiers are guarding the front door when ropes, falling from the ceiling, surprise them. As Donald helps Tony to the ammo dump a few feet in front of them, four of the team members are traveling down the ropes, easily taking out the guards. Donald comments on how that the other members of the team are extremely good at fighting and Tony tells him that he needs to get used to seeing fighting. Tony walks down the stairs of the Ammo Dump and comments on the great luck of being able to find the armor and weapons that may help them win the battle. As the team finds weapons and armament that suits them, Gwen tells Blake of her regrets for not being able to go with him to warn the High Council. Blake interrupts her, saying that none of them ever had a choice in the matter once the war had begun. Stacy tells Blake of her distrust in Doom, who has agreed to escort Blake back to the High Council’s hideout. Doom tells Stacy that the Council would not recognize her in his stead, so he must go to help Blake. Ben hops on one of the two hover-bikes that have been stored in the ammo dump and tells Gwen of his distrust in Doom. However, they have no choice because at the moment all they have left is each other. As Ben and Susan ride one bike, Gwen and Tony fly the other to the bridge of Mikhail’s ship.
A man whose name has been lost to his talent, who know calls himself Bullseye, leads hundreds of humans from the cell blocks below, each one fighting for their very freedom. Bullseye commands the others to keep moving forward to the airstrip on Mikhail’s ship. The enemy of Bullseye’s crew maintains the high ground though, as they begin to kill thirty humans to their two from their position of power. Luckily for the humans, Ben Grimm has the higher ground than even the traitorous humans. Using the laser cannon on his hover bike to destroy the tower and all the enemies on it, he ensures Bullseye’s team’s victory. Emerging victorious, the transport arks are now under the control of the humans. As Ben and Susan fly away, the humans below cheer their victory.
Aboard the auto-bridge B-2, a handful of traitorous humans react to the spreading alarms, but seconds too late. Tony and Gwen bust into the room, killing the humans as they are busy trying to find what has set the alarms off. Tony tells Stacy that she needs to buy him some time as he … just then Tony turns around to see the Thing holding an unconscious Gwen. Menacingly, the Thing tells Tony that his time is up.
Meanwhile, Mikhail stands above what is left of the Human High Council. He talks to them about giving them one more chance to bow to his leadership, or they will be broken. As Mikhail talks, Donald Blake steps in. As Mikhail stands shocked about Donald’s appearance, Blake tells Mikhail that the council does not have to fear him anymore. The resistance has taken Mikhail’s ship over. As Mikhail looks to the sky towards his ship, he sees a large explosion coming off of the starboard side and he knows that Blake is speaking the truth.
Seconds later, four members of Mikhail’s Stryfe-Force bursts through the window, ready to follow Mikhail’s commands. One of the members is Marta, Rafe’s wife who had joined Mikhail’s augmentation program earlier. Like her, each member of the Stryfe-Force seems to be newly techno-gifted humans that have been programmed to follow Mikhail’s orders. Mikhail commands his Stryfe-Force to kill the council members, but they try to fight his order, telling him that they cannot kill the Human High Council. Mikhail angrily tells his Stryfe-Force that he is not asking, he is commanding. Mikhail uses his powers of cyber-organics to manipulate them into holding their guns up to the council’s heads. “God help me!” one of the members says as a bullet is heard. Luckily for the council members, Blake was not the only one to arrive, Doom came also. As the prayer is answered and the Stryfe-Force members fall to their feet dead, Doom thanks Mikhail for the use of his ship, as he pilots Mikhail’s own personal flagship just outside the window of the council’s hideout.
Below the Council, a man named Rafe holds his son in his arms as he sees the growing storm of Stryfe-Force members verging on him. Along with the hundreds of others, he can only seek shelter and hope for the best.
The Keeper stands above Empath, watching the boy writhe in agony as he most likely empathically feels every sorrow and every pain of the entire populace below him. The Keeper tells Empath that he should calm down because he is just making more work for everyone else. Just then, whether by accident or choice, the Keeper’s hand and Empath’s hand brush up against one another. In that moment of contact, Empath tries to show the Keeper just a sliver of the pain that he has had to endure these past few months under Mikhail’s torture. Only one of them has he ability to act though and as Empath screams “NOOO!” The Keeper grasps his billy club high in the air and brings it down swiftly, killing the boy. As Empath dies, Matthew Murdock kneels to the ground and rips his visor from around his eyes. As a final torment, Murdock realizes that the visor did not give him his second sight, he had it all along thanks to the accident when he was young that caused his blindness. Murdock cries as he realizes all this, for now Murdock has truly become a man without fear.
On the ground below, humans are frozen in terror, as they no longer have Empath controlling their emotions. They realize that people are dying from the Stryfe-Force’s ruthless attacks. The man named Rafe runs to save himself and his child, but as he is shot down by one of the many robots patrolling the streets, the last thing he hears is the cry of his child, who has now become an orphan. Luckily for the child, a man named Benjamin Grimm is close by and, as he drops down a ladder to pick the child up, he tells him that “Unca Benjy’s Got Ya! Calvary’s come to town…” The cavalry also arrives for the others, as hundreds of ships hover over the city dropping ladders for thousands of refugees to climb.
As the thousands reach for the sky, one man tries to ensure their survival. His name is Tony Stark and right now he has a large gray monster named the Thing coming closer to him, threatening to kill him. Behind the Thing, Gwen stands to her feet, taking up a gun and shoots a blast directly into the back of the Thing. The Thing turns and smiles at Gwen, telling her that she is as good as dead. As Gwen jumps through the door behind her, to get away from the Thing’s punch, the Thing comments that Ben and Susan must have told them about their recent encounter with him at the field base. Even the knowledge of that, he tells her, will not save her now. The Thing stomps his massive foot on the ground, causing an Earthquake that knocks Gwen off her feet. Behind the Thing, Tony tells him that she has done her job by giving him enough time to breach the ship’s security shields. “Good Lord!?” Tony whispers, as he sees the monitor in front of him and he is shocked to see, as he says a loud, that the sea wall has been launched.
At the heart of the storm, Mikhail calmly masterminds the destruction of the surrounding area, using his powers to control his entire Stryfe-Forces to pull their strings to follow his bidding. In the hideout of the Human High Council, the members stand back to back for the first time in ages, fighting with all their might against the hundreds of robots sent after them by Mikhail. Amidst the fighting and the chaos, Dr. Blake massages the hair of a fallen Stryfe-Force member as he says aloud that they are all humans and how insane it is that they are fighting one another.
Doom’s cold stare never leaves the presence of Mikhail, as Doom kills the last of Mikhail’s Stryfe-Force. Mikhail laughs about how easily Doom kills his own and how Doom is just a tin soldier that would not dare challenge Mikhail himself. “NO!” Donald Blake cries as he strikes Mikhail from the back. As he does this, Blake commands Doom to escort the Councilors to safety, because the fight is between he and Mikhail now. “Dream on gene-joke”, Rasputin tells Blake as he prepares to strike back. Donald admits to Rasputin that, in his dreams, he soars the skies and drinks amongst gods and goddesses, but in reality he is only human in a role he never wanted. As Blake summons the strength from out of nowhere, he shoves his staff through the body of Mikhail, knocking both combatants from the top of Big Ben all the way to the ground below. As the two fall, the last thing they see is the coming of Apocalypse’s sea wall, the doom of all of Europe.
Ben Grimm runs through the streets of London, being shot at by one of the many robots patrolling the city. Ben talks to Susan over their comm-link as he holds tightly to the little child in his arms. He hears Susan tell him about the sea wall and how if he cannot make it to their ship in enough time, they will have to leave him. Ben makes it to the ladder of the lead ship just as Stryfe-Forces blow up a nearby transport ship, one of the last casualties caused by Mikhail’s forces.
Above the lead ship, the Thing stands behind Tony, shocked to see that Apocalypse has betrayed him. Tony turns to the Thing and tells him that the betrayer has now been betrayed. Addressing the Thing as Dr. Banner, Tony tells him that they need the man now, not the monster. As the Thing turns back into Dr. Banner, Gwen is shocked to see the scientist who ran the field center was actually the monster responsible for so many people’s death. As Tony holds back Gwen’s gun, Banner asks how Tony knew it was he. Tony replies that his allies are not stupid and the same injuries inflicted on the monster was the same that appeared on him as well. After Banner walks to the consoles, he quickly patches through to Susan, who is piloting the lead ship and programs the ship to be able to control all the other ships around them to better evacuate the civilians. Susan’s face appears on the console before them, informing them that Banner’s efforts were successful. At the same time, Doom walks onto the ship, followed by the members of the council and commands Tony to turn the ships around and head towards Apocalypse’s citadel to take the last fight to him. “NO”, Tony tells Doom, he says that their first priority is to the civilian’s relocation because none of them set out to be “Avengers!”
Gwen sees Doom has broken his promise about coming back with Blake and takes her anger out on him by striking Doom to the ground. Susan, piloting the ships to safety, turns to look at Ben who had just recently arrived and she tells him that they have finally done it and they may just make it yet. Susan is shocked and heartbroken to see a bullet wound through Ben’s chest and her friend dead. The young child is alive though, and is still embraced in Ben’s arms. The child cries and lifts his arms towards Susan, as if to ask her to hold him.
As the convoy races to escape destruction and head towards space, Gwen asks where they are going? Banner replies to her that they won’t know until they get there. Doom coldly tells them that the sea wall is approaching their flanks and they all may still die. Ignoring him, the friends and members of the High Council watch towards the skies.
Susan reaches towards the child and, as she grasps the boy, looks down to see the child’s nametag. On it, the letters read “Frankie”. As tears come to Susan’s eyes, a blinding white light covers them all and reality passes.