In the coming weeks, Emmett makes good use of his time practicing with his newfound strength and cybernetics, and helping Athena take out mutagen variant shipments around Belport. The variants are still being distributed by a third party. A fellow mask is defending the shipment and in the resulting fight, Emmett’s whip is damaged.
Dr. Venture shows Emmett how to repair the damage, and the two also begin working on a quick-connect system for Emmett’s arm that will allow him to swap out mods within seconds instead of minutes. After some debate, Emmett settles on a connection system that will allow for more potential as his capabilities grow. Emmett also takes his second mutagen variant from the raids—something that will boost his resistance to poisons.
While Emmett is working hard, so is his roommate. Lock’s progress grants him an ominous meeting with one of the heads of Gnosis—a super powerful enough to unsettle Lock.
The next evening, Emmett and Clara go out to the abandoned warehouse district to test out her exosuit and Emmett’s mods. During that time, they are approached by a patrol—two low ranking members of the Summit of Heroes. When the psychic (Serenity) tries to read Emmett’s mind, Emmett is able to break free of her paralysis and use his prosthetic arm and pistol to fire at her, knocking her out of the fight with a nonlethal round. Then he helps Clara subdue the other magic ring-wielding cape (Hunter Nine).
Serenity retreats to a Summit substation and reports the incident to her supervisor, a fellow psychic that wipes the names of Emmett, Clara, and Dr. Venture from Serenity’s memory. Hunter Nine is furious and they are left without leads.
Lock’s powers are found out at the Dionysus Club where he works and the manager is forced to let Lock go. Lock isn’t too upset because now he has a better paying job through Gnosis. His internship has been upgraded…
While Emmett continues rounding out his weapon loadouts, Dr. Venture becomes increasingly worried about TINA’s development. Though Dr. Venture gives her direction, she’s taking more of an active lead in research and development. Dr. Venture worries that he may have two unique and potentially dangerous technologies on his hands: TINA (a true AI) and Emmett (a 100% nerve-integrated cyborg).
While Emmett continues working on his final semester of college, TINA contacts him and recommends several upgrade paths for the rest of his body. Emmett is excited before he learns that this is one more step that TINA has taken without Dr. Venture’s explicit directives… Emmett eventually settles on modifying his skeleton—an intensive procedure that will lace his bones with a titanium alloy. The surgery is successful, and though Emmett’s recovery is fairly quick thanks to the Mutagen-A in his system, he has some worries that most of the procedures won’t be reversible. He begins to wonder just how far he will go and what he will become.
When Emmett finally goes back out into the city, he meets a quirky gadgeteer named McGuire, who challenges him to a sparring match. The match ends with Emmett getting knocked around and McGuire getting tasered, then the two bonding over a mutual love of tech.
Lock comes home that evening, visibly shaken after having “a rough night” of work. In Lock’s chapter, it’s revealed that he killed several people as part of his new job with Gnosis. He is shook up from the ordeal, both because of what he did and how easy murder has become to him.
In subsequent tests on Emmett’s health following surgery, Venture confides in Emmett just how revolutionary his prosthetic arm and nerve connections are. Emmett wants to help the world by being a super, but the technology they’ve developed could soon help thousands of amputees.
Clara briefly runs Emmett through a program of mindfulness and yoga to help him resist psychics and illusionists.
Wight visits Venture in the lab again, this time warning him about his proteges’ run in with Summit capes. They talk briefly about the flooding of mutagen variants onto the streets of Belport. Venture suspects it is an inside job because the leak is simply too big.
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In the interest of time, Venture confides in Emmett and Clara that he and TINA have developed tracking programs that can trace individuals through their phone usage. He plans to use it to figure out where the mutagen shipments are coming from. In the same visit, Emmett undergoes another upgrade—another infusion of nanomachines that will increase all of his blood and white blood cell functions.
In preparation for their mission on the mutagen manufacturing warehouse, Emmett enlists the help of Athena. She meets with Emmett, Clara, and a holographic Dr. Venture to discuss their plan. While they wait for the trace to be complete, the group knocks out another shipment and we see a point of view from Athena as she fights a gravity-warping super. Emmett takes a cold resistance mutagen.
A chapter from Pythia’s point of view reveals their further plans and regret from their previous mission where they poisoned Amarque. They want to affect change in Belport, but they might have went too far. Their next mission is merely to destroy technology in an Aquarius corporation building.
McGuire is recruited to their cause. Emmett and McGuire have a brief fight with several supers (Cherry and Larian), who are revealed to be friends of McGuire.
Shortly after, Clara reveals the reason for her exosuit—her powers are fusion-based and hard to control. So she wears an exosuit that runs off of her power. She shows Emmett footage of a “meltdown” were her power undergoes a runaway reaction from overuse. It is violent, destructive, and ominous.
Emmett and Clara discuss how to take out the Mutagen-X super. They come to the conclusion that the Nonlethal Window will be small and there is a high likelihood that they will accidentally kill the super… if they can beat him. A following chapter shows Lock’s new job, hunting down escaped mutagen test subjects and killing them. A cleaning crew comes by afterward.
Emmett reads transcripts of Mutagen-X testing, revealing that eventually almost all X subjects lose their minds and need to be put down.
Emmett, Clara, McGuire, Athena, and two of Athena’s allies (Borealis and Luna) infiltrate and assault the mutagen manufacturing warehouse. They battle guards and enemy supers, including hair-girl and Feedback—both supers they had fought before at other mutagen shipments. They destroy the warehouse, but not before barely surviving and escaping the appearance of a masked Lock, who causes Clara to have a meltdown. They escape by following Clara’s meltdown into the basement and tunnels beneath Belport.
Emmett follows the masked Mutagen-X super… and finally finds out that it has been Lock the entire time. Emmett leaves and talks to Venture, and a rift forms between the two because Venture had kept it secret for so long.
Emmett goes back to the apartment and waits. He and Lock finally confront one another. Lock says that they’ve both been keeping secrets… He attacks, and Emmett stabs him with the nanomachine-filled knife. Lock slowly succumbs to the nanites, but not before nearly killing Emmett. Venture is forced to shoot Lock through the chest with a heavy drone.
Serenity, Hunter Nine, and the Summit investigate the aftermath of the destroyed apartment. Gnosis claims Lock’s body. It is revealed that Lock is in a state of suspended animation… but his survival remains unclear.
Emmett wakes up in the lab, having been evacuated by Venture’s drones. All four of Emmett’s limbs are prosthetics now. Wight visits and after an argument, Venture gives up the location of Pythia (having found them via cell phone tracking). Wight speaks with Emmett, saying that his time as a free mask might be coming to an end soon and that he’ll need to be careful, otherwise he’ll need to enlist with the Summit.
Emmett leaves the lab, stating that for the moment he cannot trust Dr. Venture and that he needs time to figure things out. He attends Lock’s funeral, but can’t bring himself to tell Lock’s sister the truth about his death. Emmett moves into a new apartment for the last few weeks of the semester.
In the epilogue, Venture goes to Gnosis to speak with the VP, Ichabod (who also spoke to Lock). It is revealed that Venture has been working closely with Gnosis during the entire story… Ichabod reveals that Gnosis has been behind the mutagen variants, leaks, and manufacturing all along and that they are pausing the enterprise. It was a means of testing dozens of new mutagens at the same time, but no “new letters” emerged. Ichabod thanks Venture for cleaning up the mess with Lock and Pythia (a creation of the mutagen variants but acting on her own whims), and revealing the nanomachine weakness of their Mutagen-X compound.
The final reveals are that Ichabod and that almost all of Gnosis are vampires. Venture and Gnosis have allied themselves in a mutual ceasefire to one day overthrow the rule of supers and upset the balance of the world. Vampires want to rule the world… but Venture wants technology to usher in a new age… Both Ichabod and Venture know that one day their truce will end.