Amazing Spider-Man Vol 1 #358

Spider-Man, Moon Knight, Darkhawk, Night Thrasher, Nova, and the Punisher are in a life and death battle against the Secret Empire and their cyborg leaders Midnight and Lynn Church. Everyone is shocked at the discovery that Lynn Church has been secretly a cyborg this whole time. She explains that the Secret Empire's former leader, Number One, was her protege. When the Empire began working on cybernetics, Lynn volunteered for early experimentation. When Jeff Wilde was enlisted for cybernetic augmentation, she was assigned to oversee him to earn his trust. She then used her position to assist Midnight in breaking free from the Secret Empire's control so he could usurp a position of power within the organization.^{[Continuity 1]} Midnight is hurt by this, thinking that he interest in him was merely business. However, Lynn assures him that her affections toward him are genuine, and she had to keep her true nature a secret after the death of Number One as she did not know how the other members of the Empire would react.^{[Continuity 2]} When Thunderball also questions his position within the Secret Empire, she also promises him a place within the organization.

All this discussion takes their mind off the battle and the combined heroes begin gaining ground in the battle. With the foot soldiers all but defeated, the heroes are ambushed by the Seekers, who are once more assisting the Secret Empire.^{[Continuity 3]} Sonic turns his attention to the Punisher, whom he almost killed in their last encounter. When Spider-Man tries to help, he leaves himself open for Midnight who fires a cryogenic beam at the wall-crawler. Fortunately for Spider-Man, his spider-sense warns him in enough time to dodge the blast. It hits Sonic instead, not only immobilizing his armor but making it incredibly brittle. With the tables turned, the Punisher shatters Sonic's armor with a single tap from the handle of his knife. Completely defenseless, Sonic is knocked off his feet by a single blow from the vigilante. The Punisher is then hit from behind by Grasp's rocket-powered fists. as Grasp rants over his hatred of costumed super-heroes, he is ambushed himself by Nova.^{[Continuity 4]} Although Grasp manages to catch Nova in a shock net, the hero hits him with enough force to knock the armored villain out.

Moon Knight decides who to help when he spots Chain choking Night Thrasher with his weapon. Spotting the remains of Sonic's weapon, Moon Knight removes the energy leeching device and snaps it onto Chain. Seeing Chain in trouble, Midnight breaks off from his attack on Spider-Man to knock the hero aside. This allows Spider-Man to lay into Lynn and ultimately sprays webbing in her face. Seeing everything falling apart, Thunderball stands back and begins to question his loyalties once again. When Lynn rips off Spider-Man's webbing she also tears off the synthetic skin that covered her metallic face. Seeing Lynn like this horrifies Midnight, who now considers her a monster for allowing the Secret Empire to do that to her willingly. Having prepared for Midnight potentially betraying her, Lynn activates the pain-inducer that had long been deactivated. Seeing things hitting the fan, Thunderball steps in to try and get ahold of the device in order to control the two cyborgs. However, Lynn is too powerful for Thunderball, destroying his new cybernetic weapons in the process. With the pain subsiding, Midnight realizes the grave error he made and decides to redeem himself by unleashing energy blasts all over the facility to bring it to the ground.

With the warehouse about to explode, Spider-Man and his allies grab the surviving members of the Secret Empire's minions and carry them outside just moments before the facility explodes. In the aftermath of the battle, Night Thrasher warns the Punisher that the police are on their way, allowing the vigilante to silently slip away. Spider-Man offers his sympathy to Moon Knight for the loss of his former partner, Midnight. Suddenly, someone begins digging their way out of the rubble. It turns out to be Thunderball, who is too injured to put up much of a fight and surrenders. He tells them that the two cyborgs killed themselves, tossing their severed arms as proof.^{[Continuity 5]} Moon Knight wishes Midnight hadn't gone bad, but Spider-Man offers some solace: At least his former sidekick died helping the good guys.