In Anderson, Indiana, two AIM agents wheel away the recovered G-TAC genetic bomb they recovered from their recently raided lab. The bomb had been hidden in an extra-dimensional pocket. As they leave the building, one of the AIM guys says that he wishes they were wheeling around a regular bomb and not the genetic type. The other guy asks what the difference is and he notes the slow and horrible deaths the people in Indianapolis suffered. The other guy argues that dead is dead. They agree to disagree and move towards their van. In a flash of teleportational energy, Sean Madigan arrives and says that he understands the distinction being made. As he shoots them both, he explains that Joe here wanted a clean and quick death and he is happy to oblige.
In Manhattan, Carol Danvers is enjoying her second date with William Wagner. Sushi and flirting is just what Carol needed after her tense reunion with Julia Carpenter. She notes that he’s ended up in the middle of super-hero craziness twice now and been okay with it, as if it’s completely normal! After dinner, the two go for a walk and talk for hours before ending up at William’s place. Carol is relieved that there are no teenage sidekicks around to interrupt things!
Carol is surprised to wake up in her own bed with Wonder Man lying next to her! She is bewildered for a moment and then hears a beeping noise. It’s her doorbell and she wakes for real, in her new room on the Minicarrier with only her cat, Chewie sharing her bed.
She makes her way to the door, calling out that she’s coming. It’s Maria Hill, Deputy Director of SHIELD. Carol had scheduled a meeting for this morning after numerous requests from Hill. Carol asks if Maria minds joining her in the gym.
Moments later, Carol is working out with a punching bag and Hill is reviewing all that Carol has been doing since setting up Operation: Lightning Storm. She is clearly not happy that Carol has requisitioned SHIELD agents, attacked AIM without SHIELD clearance and been given command of a Minicarrier. Carol tells her that Tony Stark approved all this and Maria interrupts and points out that she also used SHIELD resources to help a known felon kidnap her daughter and flee. Carol makes it clear that they did everything by the book and the custody issue is being dealt with in court. She assures Hill that she debriefed Tony Stark on all of this. Maria asks if this is the only time that she’s debriefed SHIELD’s new director.
Carol is momentarily stunned by Hill’s suggestion that she and Tony have been intimate. Hill uses Carol’s moment of incredulity to make her point: despite whatever deal Carol has with SHIELD’s new director, he won’t be able to protect her if she crosses the wrong person, breaks the wrong law or gets in her way. She then hands Carol a top secret file relating to her recent confrontation with AIM in Indiana. Carol points out that this is a bust she accomplished without full SHIELD authorization. Hill jumps right into a summary of the report. The SHIELD agents stationed at AIM’s former lab were found dead alongside a pair of AIM scientists. The SHIELD agents were killed by a device that fired all their synapses at once, frying their brains. While the AIM agents were shot by a non-SHIELD weapon. Carol surmises that there’s a third party involved and Hill agrees. Carol asks why AIM would be there considering they dismantled the lab completely. Hill tells her that under normal circumstances she’d send a team of agents to figure it out but since Ms. Marvel is determined to play super-spy, she thought maybe she should handle it.
Carol says no immediately and begins to inform Maria of the agreements she and Tony made. Commander Hill interrupts and says that she doesn’t agree with this pact. She tells Carol that the country is coming out of a dark time and they can help with that or spend their time explaining why the new director of SHIELD is making legally questionable deals with his favorite blonde. Carol is stumped by this argument. As Maria exits the gym she tells Carol that she’ll expect her report on what she finds in Indiana by the morning. Carol curses loudly and punches through the punching bag with a single blow.
Soon, Ms. Marvel and her team are in Indiana following up on Hill’s information. Carol is still fuming and Locke has to ask her to tone down her internal anger as it’s hard for her to work with all that intensity nearby. Carol apologizes. Baines reports that crazy as it sounds, it looks as if AIM has found a means of accessing the Calabi-Yau spheres. Ms. Marvel asks how that’s possible and Wonder Man asks if she’s pretending to know what Baines is referring to. Carol tells him she’d be doing a better job of faking it if he’d shut up. Baines explains that Calabi-Yau spheres exist beyond the traditional four dimensions (height, width, depth and time) and exist within the six additional dimensions that we do not normally perceive. AIM found a means to store things with these extra-dimensional holes. Simon asks what this means exactly and Carol tells him it means that AIM found a way to hide things in plain sight. He asks if she’s still acting like she understands this and she asks if the man in the leisure-suit jacket is questioning her intelligence. Baines interrupts and is impressed by AIM’s achievement but before he can say much the entire group is teleported away!
Ms. Marvel orders everyone to draw their weapons and be ready for anything. They find themselves on a platform inside an AIM facility surrounded by armed AM agents. They are ordered to power down and drop their weapons. Wonder Man asks where they are. AIM’s Scientist Supreme and leader of a rebel faction of AIM, Monica Rappaccini tells them where they are doesn’t matter but what they do next does.
She introduces herself and tells them that they are quite an interesting catch. Ms. Marvel powers up her fists with energy and begins to advance on Monica who orders the facility’s neural inhibitors activated. This freezes Carol in her tracks. Monica specifically asks that they not kill anyone as she does not want to have to deal with the Avengers coming after her if she kills their “cover girl”. She then orders her team to search the Calabi-Yau zones they transported in.
As Monica admires Wonder Man’s derriere, Carol checks with Agent Locke to see if her psychic hardware is still functioning. Locke telepathically replies that it is and Ms. M orders her to open a telepathic link between all team members. The telepathic link is open: Simon doesn’t seem to mind Rappaccini’s attentions and Agent Sum is already plotting out how to take her down. The AIM agents complete their scans and determine that the Calabi-Yau spheres in this section are empty. Monica realizes that the G-Tac bomb has been moved and orders them to send this place back now! She orders them to scan world-wide for Calabi-Yau punctures to ensure that MODOK doesn’t get it. With that, the section of the house that Ms. Marvel’s team was in is returned to its proper place.
They are all a bit bewildered and Wonder Man asks what just happened. Carol begins to explain but Baines jumps in to alert them to the fact that Monica’s AIM faction is after the gene bomb as well. Simon says that she mentioned the “G-TAC Scrambler” and Baines and Carol inform him that GTAC stands for guanine, thymine, adenine and cytosine: the nucleotides that compose DNA. Baines adds that however they’ve been using the Calabi-Yau spheres that it’s leaving a wave of destruction in its wake. Carol asks if he can track them and he replies that he can. She tells him she wants to know where the Scrambler is within the hour.
In AIM Research Base Alpha, an agent is reporting to his superior on the progress on the development of genetic monsters called Gnashers. He reports that their survival rate is increasing nicely and that soon they will be incapable of feeling full and will continuously hunt in feed. He notes that they’ve developed a taste for live meat and they are planning to acquire “volunteers”. As he says this, MODOK shoves him into the pit where the Gnashers live. The AIM agent cries out as three beasts with huge claws and teeth emerge from a darkened cave. He begs for someone to get him out of there as the beasts lunge hungrily at him.
From above, MODOK watches as the man is devoured. He angrily denounces the Gnasher project as a waste of resources and adds that modifying gorillas is a genetic parlor trick. As he rants, he coughs up some vile fluid. One of the agents reprimands the others for upsetting MODOK and orders them to return to their quarters. The agent then helps MODOK to a private room.
MODOK thanks him and the agent replies that it is his duty. MODOK inquires about the progress of the recovery team sent for the gene bomb and the agent says that there has been no further report from them since they retrieved the G-TAC Scrambler. MODOK coughs again and the agent asks if the disease is spreading. MODOK merely tells him that it is as they predicted. The agent assures him they’ll find a cure. MODOK dismisses him saying that he needs to sleep. Once outside, the AIM agent initiates a teleportation device. This takes him to a meeting with other agents. He removes his helmet to reveal that he is rogue AIM agent Sean Madigan! The cabal asks where he’s been and Madigan replies that he’s been making preparations and they are about to get their wish. MODOK will soon be theirs!
Madigan goes on to explain that they will have to fight for MODOK. These six AIM rebels want MODOK dead so they can divide AIM amongst themselves but Monica Rappaccini wants him dead so that she can assume control of the entire organization. He adds that they will also have to contend with Ms. Marvel, who is involved but doesn’t even realize how close she is to upsetting all their plans. He then raises the question of MODOK himself.
As Madigan explains all this, Monica’s faction locates more Calabi-Yau punctures in Seattle and MODOK receives intel from a mole he has planted inside Ms. Marvel’s Lightning Strike team! Each group is chasing after the DNA bomb for different reasons. Carol wants to make sure it is never used again, Monica wants to prevent MODOK from acquiring it and MODOK needs it to stave off his own death! MODOK’s body is beginning to break down due to the process that transformed him from normal scientific mastermind, George Tarleton into the giant-headed Mental Organism Designed Only for Killing. The G-TAC Scrambler can be programmed to repair the damage done to MODOK’s body, saving his life!
Madigan announces that MODOK and AIM are about to die and that he will re-organize it into a dozen nimble and more efficient terrorists cells. The leader of the cabal of rebel AIM scientists begins to protest as this was not part of the plan but Madigan tells him it’s already happening and all the involved parties will be converging on their location in moments. The best they can hope for is to gather together what’s left after the final battle and forge ahead. At that moment, MS. Marvel’s mini-carrier appears outside. Then two separate teams of AIM soldiers teleport inside.
At that moment, Ms. Marvel and Wonder Man come crashing through the window and the fight begins. Carol is identified as the primary target and Simon asks if he should take it personally. Carl banters back that she does kind of rock. One of the agents throws a small device he calls a “dark door” and then his team teleports away. Locke tells Ms. Marvel that they were all thinking they didn’t want to be anywhere near that thing when it activates. Carol goes after it, leaving Wonder Man to handle things there. Ms. Marvel flies it high into the sky as she calls on Baines for info on what the device does. He reports that it’s a localized black hole generator. Carol then realizes that it is unusually light and that it’s got to be a fake. Baines says he isn’t sure as Carol pops it open to reveal that it’s hollow inside. Realizing this was a distraction to force her to leave the battle, Ms. M heads back at full speed.
Locke informs her that something else is teleporting in. This time it’s MODOK who orders his men to kill anything that moves. He then seizes control of Wonder Man’s mind with his mental powers. Locke tells Carol that MODOK is here and she orders Simon to engage him. Locke tries to explain that Wonder Man is no longer an asset when he comes flying out to meet Carol. He slams into her, echoing MODOK’s commands as he grabs her by the throat: “Kill Ms. Marvel!”