Wolverine is under the control of Hydra and has infiltrated the ventilation systems of the Baxter Building, home of the Fantastic Four. He looks down into the garage workspace where Johnny Storm AKA The Human Torch is working on a classic car. He makes several calls to the women he is currently dating to explain that SHIELD has ordered a lockdown of the Baxter Building and to cancel his dates. Naturally, they each think that he is dating her exclusively.
As Wolverine observes the youngest member of the Fantastic Four he notes that the team has a security system that only three people on the planet could infiltrate. The Thing arrives to ask the Torch to rub some cream on his back. Johnny says to have Sue do it since he feels uncomfortable with that sort of thing. Wolverine notes that the Thing is big but he’s taken him down before.
At Hydra’s secret lair, The Gorgon wonders why Wolverine has not struck yet. An advisor assures him that Wolverine is doing reconnaissance and waiting for the proper moment to strike. The Gorgon is anxious and wonders if perhaps the upgrades that Hydra installed are malfunctioning. The advisor tells The Gorgon to relax and that everything is working properly.
Wolverine notes that the upgrades implanted in him have set the security monitors to reply the last twenty minutes, giving him a nineteen-minute window to complete his mission.
Wolverine’s true personality asserts itself momentarily and protests based on the fact that Reed Richards is a friend. Hydra’s programming kicks in to subvert these thoughts. Wolverine recalls the process through which Hydra and the Hand murdered him and then resurrected him as an assassin. He remembers that they are targeting superhumans with the intent of administering the same process on those he strikes down. Their plan is to create their own army of superhuman assassins. Baron Strucker is present at the conversion of Wolverine and orders The Gorgon to lean on those portions of Logan’s personality that lend themselves to his tasks as an assassin for Hydra. Hydra’s programming continues to suppress Logan’s natural heroism to continue their plan to target Mister Fantastic.
In his lab, Reed Richards is inside a “think tank” full of magenta liquid. His elastic body is shaped into a ball. His wife Susan Richards AKA The Invisible Woman interrupts him. She reminds him that it is time for him to read their children a bedtime story. He tries to get out of it since he is in the middle of a project but she notes that he hasn’t see their son Franklin in two days. Reed says he will do it via the intercom, which he has programmed with the ability to interact with others using his personality traits and image as well as viable answers to millions of questions. This way, he can continue his work with Tony Stark and Hank Pym while the children get their story.
Sue wonders if he uses this device to appease her when he’s too busy. Reed says directly that there’s no way she would know, much to Sue’s chagrin. As she leaves the lab, Wolverine thinks to himself that she’s the only one who makes him nervous given her powerful force fields.
Reed is “meeting” with Dr. Henry Pym and Tony Stark in a top-secret area of “non-space” that the trio of geniuses uses to discuss their latest projects and inventions. All three are linked in via sophisticated cyber-suits. They are discussing a terraformer device that Reed is perfecting with plans to use in Africa. Tony and Hank discuss the international, political and environmental impacts of the device and wonder how the UN has reacted. Reed says they’re looking at five years of trials.
As Reed explains that it took him 48 hours to develop this and what an ordeal it can be, a security alarm sounds indicating that their cyber-space is being hacked. Reed commands Tony and Hank to disconnect and then gives the word to the rest of the Fantastic Four that he has picked up Wolverine’s gene signature in the data room.
Reed gives the order to subdue Logan using maximum force with property damage an acceptable to get the job done. As Ben hears this, he picks up the classic car Johnny was working on and hurls it through the wall into the data room.
The Human Torch flames on and grabs Wolverine by the wrists, burning through flesh and urging the errant X-Man to give up. Wolverine has already had sufficient time to hack into the FF’s mainframe and initiates a security protocol to douse Johnny’s flames. Foam sprays from the walls and cover the Torch as Logan’s commands activate the Baxter Building’s systems. He pops his claws and grabs the Torch as he tells him he should have taken him out while he had the chance.
The Thing attacks with an “earth-shaker”, slamming his stone-like fists into the ground, which opens up beneath Wolverine. Logan and Johnny fall to the room below and the Thing jumps down in pursuit. He tells Logan he’ll knock out all his teeth if he’s hurt the Torch.
Wolverine has landed in an observation room where Reed monitors various timelines, experiments and dimensions. He thinks to himself that the Thing is playing for keeps and he should just let the big guy subdue him and it would all be over.
The Thing rips some cabling from the ground and lashes out at Logan. Logan thinks about how Hydra did the same thing to him that Weapon X did and tries to fight it. He realizes this has put him right back to the mental mess he was before Xavier helped him. Again, the Hydra conditioning tries to counter these rebellious thoughts.
Wolverine continues to fight and finally manages to connect, sinking his claws into the Thing’s shoulder. As he does this, the security protocols in this area activate and target Wolverine and his Hydra-inspired thoughts reprimand him for not re-writing the security systems to ignore his presence.
Meanwhile, the Invisible Woman has sent her children twenty minutes into the future to keep them safe from the conflict. As Wolverine fights off robotic drones, his Hydra programming kicks in, detailing the futility of such resistance and Hydra’s ultimate goal to use the world’s heroes to undermine the world’s governments and institutions for their own gain.
Mister Fantastic arrives to confront Wolverine. Reed envelops Logan in his elastic body, hoping to contain the X-Man until SHIELD arrives to help set things right with him. Wolverine mentally requests a jump from Hydra command, unwilling to give up against Richards. The Gorgon notes that they can only move him sixty feet, which the tech advisor assures him, will be enough.
Wolverine is teleported remotely and emerges in an outer hallway where he is attacked by more guard drones. He suddenly freezes up as he feels his lungs freeze up. He catches the scent of Christian Dior perfume and realizes that the Invisible Woman is responsible. He switches to infrared sight as Sue explains that what he’s feeling is a pair of her force fields resting inside his lungs. She explains that if he doesn’t stop what he’s doing, she’ll double their size. She lets him know in no uncertain terms that she doesn’t care if he’s sick or mind-controlled; no one enters her home and threatens her family. She then turns his optic nerves invisible and renders him effectively blind.
Realizing he’s been effectively trapped, Wolverine mentally orders Hydra to scratch the original plan and shoot for a specific spot nearby. An explosion rocks the corridor, sending the Invisible Woman to the ground and breaking her concentration. Sue looks up to see Wolverine clinging to a small Hydra shuttlecraft, which is zooming away from the Baxter Building.
The Human Torch pursues Wolverine who is still having trouble seeing. Despite this, he dives from the shuttlecraft and attacks the Torch in mid-air. He makes a mental note that Hydra got what they came for already as he collides with Johnny Storm. Wolverine drives the two to the ground near a gas station as his own flesh burns away. The gas station explodes into flames.
Sometime later, emergency crews are dealing with the fire. They discover a survivor who identifies himself as the Human Torch. He’s been badly burned so they load him into an ambulance. As they do so, claws pop out of the bandaged form. At the site of the fire, the remaining members of the Fantastic Four are told by the fire chief that the Torch has just been loaded into an ambulance. As they receive this news, the true Human Torch emerges from the fire. Realizing that the medical team has been duped, the chief calls in to dispatch and is told that ambulance is still on standby. The ambulance is now empty, its crew incapacitated.
In the Hydra base surrounded by monitors with the faces of Earth’s heroes on them, the technical advisor reviews the mission. He orders that AIM be notified that they now have the disc with Reed Richards’ most radical ideas and they want these ideas developed into weapons immediately. He orders the Hand to step up their plans and wants ten more superhumans converted into assassins within a week. He then commands his agents to find Wolverine and bring him in for his next mission: an assault on Tony Stark and the heart of the US banking industry.
He notes that he wants this all in motion immediately since Hydra’s secret bankroller arrives at midnight and he wants this all in order for her arrival. He finally is fully revealed as Baron Wolfgang Von Strucker himself!