Sean Madigan speaks directly into the camera. He introduces himself and reveals that he is the son of George Tarleton. He admits he doesn’t know much about his father except that he is nothing like him. He explains that his mother, Linda had an affair with George in college and that he abandoned her when he found out she was pregnant with his child. George went on to work for AIM as a mere technician until he was transformed into MODOK. He notes that it was George himself who declared MODOK a “Mental Organism Designed Only for Killing”. Sean declares that he was the one who strapped a DNA bomb to MODOK and dropped him in Times Square and that he’d bet that MODOK wished he had never abandoned him now.
In Times Square, police have surrounded MODOK and called for assistance of the superhuman variety. Aboard Minicarrier 13, Ms. Marvel and Wonder Man lead AIM Supreme Scientist Monica Rappaccini to the bridge where an Avengers alert had just sounded in response to the threat posed by MODOK. Agent Baines asks what she’s doing there and Monica asks if he’s the one who cracked their teleport protocols. He responds that he did and starts to explain further in a snappy retort but is cut short by Carol. The automated Avengers alert informs her that a Level 3 threat has surfaced in New York City and asks that all Avengers respond immediately. Unfortunately, they are currently over Seattle and three hours flight time to NYC. Wonder Man and Ms. Marvel realize that even under their own power they couldn’t reach New York any sooner. Carol turns to Baines and asks if he might be able to replicate AIM’s teleportation process to get them there quicker. Monica laughs at the idea that Baines could accomplish this. Ms. Marvel snaps at her, telling her that she can choose to help or go back to her cell.
Five minutes later, Minicarrier 13 hovers over Times Square courtesy of Agent Baines’ technical savvy. As Ms. Marvel leads Wonder Man, Agent Sum and a pair of armored SHIELD agents towards MODOK, she thinks about how satisfying it was to see Baines wipe the smirk off Rappaccini’s face when he managed to duplicate AIM’s teleportation effect.
As they hit the ground, Carol orders Sum to secure the perimeter and the agents to pull back local law enforcement. As she hands out assignments, Wonder Man notices the G-TAC Scrambler strapped into MODOK’s hover-chair. Ms. Marvel asks what kind of sick-o Madigan must be to do such a thing. A countdown has been initiated and MODOK laughs as he sees that Ms. Marvel and her team have walked into a trap. Carol and Simon realize this and Carol immediately orders everyone to get out of there.
She powers up a photon blast and Simon asks if she just plans to blast him. She asks if he has a better idea and he barely has time to answer “Not really” before being hit by a laser blast from MODOK. Her blast bounces off and MODOK laughs at her and tells her that he hopes that he did not bruise Carol’s “plaything”, referring to Wonder Man. Carol replies “Laugh it up, Mr. Potato Head” as she ponders which limb to rip off first. At that moment, the G-TAC Scrambler activates, cascading the area with mutagenic energy.
Meanwhile aboard the Minicarrier, Agent Baines cries out when he sees the gene bomb detonate. Monica stands nearby and tells him that he planned the whole thing. She tells him there’s no need to maintain his charade with her. She tells him to deactivate the teleportation block so that she can get out of there. He tells her that it isn’t what she thinks.
She confronts him about his secret alliance with Sean Madigan and accuses him of plotting this entire scheme. He yells at her that he doesn’t have time for this as he opens a SHIELD channel to call for backup. She stops him before he can give the location by bashing him in the head with her heavy, metallic handcuffs. He is knocked unconscious and she takes his gun from his holster and shoots him. As she kills him, she bids him farewell and tells him that she’s off to have words with his master.
Below, Ms. Marvel grabs hold of MODOK and lifts him into the air. As she does so, her body is irradiated by the energies released by the G-TAC Scrambler and she begins to mutate. Her muscles expand and she becomes a monstrous, hulking version of herself. MODOK mocks her, admitting that he knew of his son’s role in all this. As Carol mutates, the voices that have been plaguing her whenever she is in grave peril begins speaking once more. They note that she is mutating at the root level and that if they do not reverse the effects immediately she will terminate. Her skin turns blue as she punches MODOK’s chassis propelling him into space. He shouts that his son is more like him than she knows.
The voices in Carol’s head state that they will perish as well if Ms. Marvel dies. She responds to their words and asks who they are. She tells them she can hear them talking. They are surprised by this and declare that this is unacceptable! At that moment, Ms. Marvel is overwhelmed by the pain caused by the mutation running rampant through her body. She cries out and loses consciousness. Wonder Man sees her begin to fall and flies up to catch her. Her body has already starting to revert to a less muscular form, though her skin is still blue and her eyes now glow with an eerie red light. Simon asks her if she’s okay. The voice that responds is not Carol’s! The mysterious voice that Carol has been hearing tells Simon that Carol’s genetic code was damaged before their interface could be activated and that they are doing their best to repair her.
Simon is shocked to hear this and rushes Carol back to the Minicarrier. He tries to hail the ship but communications are down. By the time he reaches the hangar, Carol’s body is nearly back to normal. She comes to and asks him to put her down. She’s a wobbly and then collapses to the floor, vomiting blood. She then loses consciousness again.
Elsewhere, Sean Madigan is transmitting a live address to the various active factions of AIM. He declares that the time of MODOK is finally over and his tyranny is at an end. He tells them all that AIM was once about ideas. Their goal was to break down social, political and religious barriers and craft a world ruled by intellect. He points out the sloppy and pointless attack by MODOK on Times Square and asks what this could help them to achieve. He declares that they can no longer operate as a single organization. That they are better served in reaching their goals if they act independently as separate creative cells. He tells them to trust no one but those they share their laboratories with. He tells them that they can accomplish what MODOK could not. He then pauses as someone teleports into the room. He greets her with a surprised hello. He is then shot through the head! Monica Rappaccini blows the smoke off the gun and says simply “Goodbye”.
One week later, Carol sits alone in her quarters surrounded by boxes that have still not been unpacked. She knows she needs to write up a formal report but she can’t bring herself to do it. She realizes that with everything that has happened, she had no control of any of it. She wonders how she is supposed to lead the Avengers when she can’t even get a team of SHIELD agents through a basic encounter with AIM in one piece. Rather than give in to self-pity, she reviews the final outcomes of the past week. Madigan is dead and AIM is in disarray and MODOK is out of the picture… for now.
AIM is now plagued with paranoia and infighting. Monica Rappaccini has seized control of roughly 25% of AIM and is struggling to maintain control. Carol admits that she loathes the woman. Early that day, Carol attended the funeral of Agent Baines and presented his family with flag from his casket. They uncovered that Baines did betray them by deactivating the teleportation lockdown and allowing Madigan and MODOK to escape with the gene bomb. It turns out that Baines knew Madigan from years earlier and that he owed Madigan money. Madigan called in the debt and Baines reluctantly agreed to help him now. Carol made sure that his betrayal was kept off the records. Agent Locke was de-commissioned and placed on medical leave. As a result, her cybernetic enhancers were surgically removed. She is recovering from multiple surgeries in Seattle. Carol admits that she should visit her but doesn’t think that she’d be too happy to see her at the moment.
Carol herself has had to deal with plenty of hospital examinations following the incident with MODOK and the gene bomb. Despite exhaustive tests, she still has no idea why she mutated into a blue-skinned, red-eyed monster or how it is she spoke in voices other than her own. Every test has shown the same results: she is perfectly healthy. She wonders how she can trust or if necessary, fight her own body.
The good news is that Agent Sum has requested to stay on with Operation: Lightning Storm. Carol is still curious about his apparently enhanced abilities but can’t help but admit that he’s a keeper. Carol makes her way to a training room where she works out her frustrations and doubts the old-fashioned, superhero way… by punching something. She pummels a reinforced metal wall until her hands bleed. She feels like giving up and crawling inside a bottle but she knows she can’t. For once in her life she has a worthwhile direction and the resources she needs to accomplish her goals. She knows that everyone is watching and waiting for her to fail. Her only response to this is to grit her teeth and say “Well, keep watching.”
Carol wishes that she could talk to William Wagner but he hasn’t been returning her calls. She can’t help but wonder if seeing her transformed into a blue-skinned brute on national television might have freaked him out. William has been deterred from pursuing his fledgling romance with Carol after being confronted with his true identity by her publicist, Sarah Day. He reviews the copy of the file she gave him which verifies that William Wagner is an alias. His real name starts with “Ro” but the rest of the name is covered. Whatever the file contains, it’s enough to get him to rethink his courtship of Ms. Marvel.
As Carol wrestles with her feelings for William, Simon stops by to check on her. He notes that he hasn’t seen her around much the last few days and that she has yet to unpack. She tries to evade his questions and there’s an awkward pause. He tells her that he just wanted to see how she was after the whole “blue thing” that happened when they fought AIM. Carol tells him that she just needs some quiet time, what with Baines’ funeral and all. She tells him she needs time to sort things out and suggests that he take a few days off from Lightning Storm. She adds that there’s no need for him to hang around here. He’s a bit surprised and perhaps hurt by this but tells her that he understands. He asks her to give him a call and maybe they could do something. Carol replies sure but it’s clearly half-hearted. After Simon leaves, she plops down on her bed. She takes her cat, Chewie in her arms and asks him if this will ever get any easier.
In a secret AIM lab, two typical AIM scientists are examining their latest project. One thinks their test subject is amazing, the other thinks it’s sort of gross. His partner chides him and that what they are doing is exactly what Madigan was talking about. Big ideas that will change the world! The other agent replies that he wasn’t sure that Madigan realized when he said that that he himself might end up being one of those big ideas. His fellow agent retorts that this lab has always been involved with reanimation and asks him to hand him the “M.G. chip”. He adds that raising the dead is about as big an idea as you can get and that they’ve been working in the field since before AIM splintered into so many disparate cells. He brags that they took what they learned from the Targoths regenerative properties, combined that with the Doomsday Man’s neural links to create something entirely new! They install the aforementioned chip into the hole left in Madigan’s skull by the bullet that killed him. They have fitted Madigan’s skull atop some kind of black and gold armored suit. They then place a glass helmet over the skull and it fills with an eerie purple gel that surrounds the skull and glows softly. One of them suggests that they call the resurrected “spawn of MODOK” the “Black Skull” but the other insists on calling him Head Case. His partner agrees and says that it’s a perfect “old school AIM” name and that Sean would approve. “Like father, like son” the other scientist proclaims.