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When Project: P.E.G.A.S.U.S.'s central headquarters in upstate New York shut itself off from the rest of the world without rhyme or reason, Captain Jill Harper and her elite Guardsman Alpha Squad (Hoss, Two-Ton, Doc, Mainframe and Soapbox) were sent alongside the hero Battlestar to investigate. After a Guardsman named Mainframe managed to override the security lockdown that had shut the facility off, Jill and her team save for Mainframe moved in, not realizing that they were already being stalked by a super-speedster, and eventually stumbled into the center point of a four-way passage covered in bloodstains and brain matter.

While attempting to figure out what could have caused such carnage, a very short figure shrouded in darkness appeared in one of the passageways and rushed at Jill and her team, revealing himself to be a zombified version of Tom Thumb, whose head was blown apart by a shot fired from Hoss' gun. Doc's inspection of Thumb's corpse revealed that he had already been dead for quite a while when he tried to attack the group.

As Jill and her team moved further into the facility, they managed to find several scientists hiding in a room looking over a series of blueprints that could perhaps show them a way out of the facility. While some were terrified of Jill having shut off the lockdown, others saw hope but when one of the scientists ran to greet Jill, he was attacked by a zombie Nighthawk, who had been looking to get his hands on the blueprints and quickly began biting every scientist in sight, save for one.

When Jill attempted to shoot Nighthawk, a hauntingly familiar voice told her not to do so in the event that she might hit a volatile energy source, when Jill and her team turned to face the owner of the voice they found zombie versions of Hyperion and The Squadron Supreme blocking the entrance off. Doc, who thought they were merely sick and wanted to help them came closer to them, only to have his arm bitten off by Hyperion, who began eating it, thus confirming the Squadron's status as zombies.

Jill shot Hyperion with an energy blaster, which was deflected by Hyperion's invulnerability and caused a large recoil effect that sent Jill falling to the ground. Hyperion and the rest of the Squadron launched into battle, with Hyperion preparing to eat Jill, only to find himself bouncing off of Battlestar's shield. While the others took on The Squadron Supreme, Jill joined the only surviving scientist and Soapbox on the sidelines, watching in horror as Two-Ton was ripped to pieces by Hyperion, who shared the spoils of combat with the other Squadron members and as the fallen scientists rose from the dead as zombies.

The living scientist provided Jill with a rather large chunk of Argonite, Hyperion's greatest weakness, and tossed it at him, causing him to become extremely ill. With Hyperion being drained of his power and the other Squadron members distracted, Jill, Hoss, Soapbox, Battlestar and the nameless scientist made a run for it and sealed the Squadron inside the room with a detonator on the door designed to explode should they attempt to burst their way out. Shortly afterward, the scientist explained to Jill and the others how this catastrophe began.

After the explanation, Jill learned from the scientist that there was one other Squadron member roaming about: Nuke, who had immediately went after the Nuclear Disposal Team and proceeded into the Radioactive Waste Chute, placing the atomic component of this crisis far beyond red. The scientist eventually lead Jill and the others to a room where Dr. Mortimer Dauoi, the man responsible for the creation of zombies, had been keeping a mysterious energy source he found while cultivating Zeta Rays in its own generator.

Upon closer inspection, Jill realized that there was something in there, but did not know what. Jill ran over everything that had happened in the hours since their arrival with the scientist as well as the information she learned concerning Dauoi's experiments and the enigmatic power source stored in the generator. Unfortunately, everyone's rest period came to an end when The Whizzer appeared out of nowhere and ran off with Soapbox while Shape came out of an air duct with the explosive in hand.

The two zombie Squadron members were quickly joined by Blue Eagle, who killed the unnamed scientist as well as Power Princess, with little time to spare Jill and Hoss locked themselves in the room with enigmatic energy which Jill decided could be used as a weapon against the zombies. Sure enough, when Jill unleashed the energy, it coalesced into human form and brought the hero called Jack of Hearts back to the world of the living. Unfortunately, Jack had lost his memories and passed out shortly after being reborn.

With little time to spare, Jill and Hoss decided to make a getaway and, under Jill's orders, were taking Jack with them much to Hoss' displeasure. Elsewhere, Nuke had broken his way out of a nuclear power plant in a small town somewhere in West Vermont and exposed the townspeople to the radiation in addition to the zombie virus which he managed to spread to nearly everyone in the town. Former Lieutenant Colonel turned Mayor Tom Aldrin contacted Jill about Nuke's invasion who told him that containment now superseded survival and that his only option was to adjudicate with extreme prejudice.

In the end, Aldrin called a nuclear strike and alongside his wife, Cathy, sacrificed their lives to annihilate Nuke and the infected townspeople. As this was occurring, Power Princess had managed to break into the room where Jill and Hoss were removing Jack from. Golden Archer, who was forced to use his teeth as arrowheads to replace those he lost, fired a shot into the back of Hoss' neck and infected him with the virus. Jill convinced him that he was too damn ornery to submit to the virus' will and gave him the willpower to resist its affects while he blew Golden Archer's head off and gave Jill enough time to escape.

Lady Lark, having lost her beloved Archer, used her sonic scream to tear Hoss asunder, however did not manage to destroy his still talking head and sent it flying towards the closing door, which was retrieved by Jill. Jill then attempted to revive Jack while simultaneously strapping a great deal of C-4 to Hoss' head along with a firing pen that, upon biting it, would detonate the C-4. Hoss explained to Jill the meaning behind his nickname, which referred to his hostile nature. Jill then spoke a poem to Hoss just as Power Princess broke her way through the door.

Jill then tossed Hoss at her, who detonated the C-4, killing Power Princess and sealing the entrance off from the others. As she finished the poem, she realizing that someone else was finishing it with her and turned around to see Jack of Hearts awake and ready for action. However, before they could take any further action Shape appeared from out of nowhere and swallowed Jill whole. Jill was freed from Shape's bulging stomach by Jack shortly afterward, whom they killed together and joined Battlestar and Soapbox in the fight against Dauoi and The Squadron Supreme.
 
Jill came into conflict with Nighthawk, who she managed to take down a few notches before Jack completely obliterated all of Dauoi's zombified creations except for Dauoi himself, who managed to flee the scene just in time and escape into the forest without being seen. When all was said and done, Jill was horrified to discover that she had been bitten and infected at some point during her fight with Nighthawk.
 
As her body began to degenerate and the infection took hold, Jill begged for Jack to end his life, but he refused to do so, not wanting to lose the one who saved him, the one he had fallen in love with. With all his might, Jack infused Jill with his zero energy and not only freed Jill of the infection but completely rejuvenated in the process, ridding her of the fatigue and physical pain this ordeal brought upon her. Jack revealed his feelings for Jill, who returned them in kind and embraced him in a passionate kiss.

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