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. Spider-Man chose the first option. By issue's end, the Gatekeeper finally showed himself. He is an amalgamation of small spiders with yellow bright glowing eyes.

In Amazing Spider-Man #507, the Gatekeeper manifests himself by having millions of spiders come out of every hiding place in New York City and swarm over nearby half a mile of prime Manhattan real estate, biting innocent bystanders and frightening others into heart attacks and seizures. After saving Mary Jane from said spiders, Spider-Man runs into Ezekiel, who once again tries to convince him to come with him to South America. Again, Spider-Man refuses. He then confronts the Gatekeeper who renders him unconscious and reveals to him, through telepathy, that Ezekiel is a pretender. This is substantiated when Spider-Man relives the moment when Ezekiel took part in a semi-sacrificial-and-somewhat-magical-ceremony, officiated by a man named Miguel, where he was granted spider-like powers. The deal, however, had one major drawback: the blood drawn from Ezekiel during the ritual 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 (i.e. Spider-Man). Ezekiel's only hope of survival was to divert the powers that he had bargained with (Shathra, Morlun, the Gatekeeper), 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 to the temple where it all began so that his blood may take the place of his when the madness and the death follows. When Spider-Man regains consciousness, he is in Brazil, outside the temple where Ezekiel acquired his powers. As he struggles to stand up, he hears a voice behind him. As he turns around, he comes face to face with Ezekiel, menacingly standing over him (looking kind of fuzzy with long fingernails), who is ready to fight him.

ACT 1: Wasting no time, Ezekiel tells Peter/Spider-Man that he intends to live and that to do so, Peter must be forced into partaking in the ritual in lieu of him. Hence, they must fight. Peter has no desire to battle Ezekiel, having somewhat idolized him in the past and having joined forces with him at various occasions to fight evil. Ezekiel is not too fond of having to fight Peter, but in order to survive, he must. So they do. As the battle rages on between the two "Spider-Men", Ezekiel thrusts a large needle into Peter's back, sending a nervous toxin into his bloodstream. The toxin instantly slows down Peter's reflexes and after a short but courageous battle, Ezekiel knocks him out.

ACT 2: When Peter awakens, he is shackled shirtless to a large column inside the temple. Ezekiel, knife in hand, apologizes to Peter for what he is about to do and slashes him across the chest using the knife. Blood immediately starts pouring out from the wound and trickles into a receptacle on the ground in the shape of a spider. Ezekiel proceeds to slash himself and his blood also starts trickling into the receptacle, mixing with Peter's. Knowing that Peter will soon be "taken", Ezekiel leaves. As their thoughts and memories begin to trade places – a downside of the ritual – Ezekiel begins to relive every moment of Peter's life, before and after he acquired his superpowers. Soon, he realizes the pain and suffering Peter has had to go through his entire life (e.g. being bullied at school, his Uncle Ben dying, the death of Gwen Stacy, etc.) and what little adversity he, Ezekiel, had to encounter through his entire life. In a moment of repentance, Ezekiel turns around and heads back towards the temple. Meanwhile inside the temple, covered in blood, Peter struggles to break the shackles holding him in place. His attempts are fruitless; a gigantic spider, sliding down a web line, suddenly appears and gets ready to take his life. At that precise moment, Ezekiel arrives and offers himself up instead. The spider drives his fangs into Ezekiel and reclaims the blood that was once his (i.e. the spider's). Ezekiel is then enveloped in silk webbing and laid to rest in the temple. Miguel, the Inca descendant that took part in the ritual ceremony that granted Ezekiel his spider-like powers, shows up and helps Peter to take off his shackles and heal his wounds. The issue ends with an image of Ezekiel, wrapped up in silk webbing, lying down on the floor of the temple.