In Amazing Spider-Man #55 (496), Ezekiel returned to New York, only to make a brief appearance that served no purpose whatsoever.

In Amazing Spider-Man #56 (497), Spider-Man began investigating the disappearance of one of his students' older brother, who had just been released from prison. When he found him, he also found Ezekiel, who explained that he had begun recruiting ex-inmates who studied and read great books during their stay in prison. However, the purpose as to why Ezekiel was doing it was never revealed. Spider-Man and Ezekiel parted ways amicably and did not see each other again until Amazing Spider-Man #506.

In Amazing Spider-Man #506, more was revealed about Ezekiel's shady past as we saw him venture to an old temple in the middle of the Peruvian Jungle where he struck a deal with a man named Miguel, a descendant of Inca Kings, who magically – or so it seemed – endowed him with the spider-like powers he now exhibits. Back in New York City, Mary Jane Parker was looking for a new challenge and an opportunity presented itself in the form of a Broadway Audition, courtesy of Aunt May and – to a certain extent – Ezekiel. Ezekiel also revealed to Peter why he came back: to alert him that the "third threat", which he had been warning Peter about for the past several issues, was about to take place. Ezekiel gave Pete two options: (1) to stand his ground and fight the Gatekeeper (i.e. the third threat) or (2) come with him to South America. By issue's end, the gatekeeper finally showed himself. He is an amalgamation of small spiders with yellow bright glowing eyes.

ACT 1: Peter is sound asleep, reminiscing about an earlier conversation with his wife, Mary Jane Parker, where she reveals to Peter that she will be auditioning for a Broadway play. His dream, however, his somewhat different from what really occurred. In it, countless spiders start pouring out of Mary Jane's ears, mouth and eye sockets, just as Peter awakens to the sound of the phone ringing. It's Ezekiel. He tells Peter to turn on the television. The images speak for themselves. Millions of spiders have come out of every hiding place in the city and have swarmed over nearby half a mile of prime Manhattan real estate. Thousands of people have been bitten by the spiders, and hundreds more have been frightened into heart attacks and seizures. Wasting no time, Peter switches to Spider-Man and heads out. He knows for a fact that Mary Jane is at her audition right now and that the spiders are heading that way.

ACT 2: Meanwhile at said audition, it is Mary Jane's turn. She starts reading the part, but is unexpectedly interrupted when a car, covered with an innumerable amount of tiny spiders, comes crashing through the front window. All those present at the scene start running away and exit through the back door. Mary Jane, the last one to exit the building, comes under attack from the spiders. Fortunately, Spider-Man drops in and rescues her. He drops her off on the rooftop of a nearby building and web-slings away. Soon, he runs into Ezekiel, who again tries to convince him to come with him to South America. Yet again, Spider-Man refuses. A scream from the street down below cuts their conversation short. A young woman is overwhelmed by thousands of spiders. Spidey drops down and comes to her aid. On cue, the Gatekeeper manifests itself and takes shape. The spiders are too many and Spider-Man falls. Strangely, the spiders start communicating with Spider-Man telepathically. They tell him that spiders are hunters and that the blood of their preys is the milk of the world. Then it is revealed why Peter was "chosen" to be Spider-Man. It was more than just a simple coincidence that he was bitten by a radioactive spider at the science exhibition many years ago; it was actually meant to happen. The irradiated spider "chose" Peter because Peter was a hunter without teeth, filled with rage, who suffered every casual wound, whether it was being tripped, trapped, struck, beaten or humiliated – all that fury Peter was forced to hold in check, for the words he could not speak and for the blind rage that gripped his heart like a vise at every fist and foot and rock that hit and kicked and cut him – who could be a better hunter than one who had been prey. Someone who would be driven to fight back against the dark forces sent by the world, who would never stop even though they were bigger and more and perhaps even stronger than he was. Because having once been prey, he would never allow himself to become such again. Would never surrender. Would take death before submission. The spider was attracted to Peter because like attracts like and the presence of the observer affects the observed, and at the end of the mathematical day, there are no accidents, no coincidences. There is only professional courtesy. The spiders also reveal to Spider-man that to see the truth, he must see the pretender.

ACT 3: The story shifts to a flashback scene where, through the eyes of a small spider dangling from a cobweb in one of the corners of the old temple seen in Amazing Spider-man #506, Spider-Man is able to learn more about the meeting that took place between Miguel and Ezekiel. Having saved Miguel's village from destruction, and as per a mutual agreement, Ezekiel took part in a semi-sacrificial-and-somewhat-magical-ceremony, officiated by Miguel, where he was granted spider-like powers. A drawback to receiving those powers is the fact that the blood drawn from Ezekiel called to the magic. The magic that was going to sustain Ezekiel, until the true one, the chosen one, was going to appear in the world. Miguel told Ezekiel that once the chosen one was going to appear, the magic was going to find him and finish the meal it began that night. Miguel also told Ezekiel that his only hope was to divert the powers that he had bargained with, to bring them to attack the chosen one, and in so doing eliminate his competition. Or failing that, to convince the chosen one to fight them on his behalf, and bring him here, to the beginning, to this temple, that his blood may take the place of his when the madness and the death follows. The story shifts back to real-time, as Spider-Man slowly begins to regain consciousness. He starts to understand why Ezekiel wanted him to come with him to South America and why each of the supernatural forces he fought in the recent past came the same time Ezekiel showed up; Ezekiel wanted him to fight them on his behalf. As our hero struggles to stand up, he hears a voice coming from behind him. As he turns around, he comes face to face with Ezekiel, the pretender.