In Sensational Spider-Man #2, Ben Reilly learns about the skeleton found in the smokestack and wonders how that can be, since he was the one who crawled out of said smokestack after Peter Parker left him there, believing that he was dead. Ben heads over to the morgue and, after authenticating the skeleton’s Spider-Man mask as being one of his creations, steals the remains.
At the end of Spider-Man Volume 1 #66, Peter and Mary Jane Parker arrive at the Daily Bugle and it is revealed that Jameson has hired Peter to get to the bottom of the whole Spider-Man skeleton story.
In Spectacular Spider-Man #232, Peter discovers that Ben has the skeleton in his possession.
In the opening pages of Sensational Spider-Man #4, Peter discovers that J. Jonah Jameson has hired a forensic expert to reconstruct the face of the skeleton. Elsewhere, Ben Reilly gets caught changing out of his Spider-Man costume by his girlfriend, Jessica Carradine, who earlier revealed to him that her father was killed, years ago, by Spider-Man (or so she seems to think). He tries to talk to her but she doesn't want to have anything to do with him. Ben later meets with Peter and the two of them dispose of the skeleton by burying it into a graveyard. While doing that, Peter tells Ben that he is suspicious of Dr. Seward Trainer, who performed the tests that revealed that he was the clone and that Ben was the real Peter Parker. Ben refuses to accept that Trainer could have done such a thing as rigging the tests.
In Amazing Spider-Man #411, the Daily Bugle puts out a $100,000.00 reward for the return of the stolen skeleton. Elsewhere, Ben Reilly has more problems than he can chew. The heat in his apartment has been shut off, because his rent check bounced, a trip to the bank reveals problems with his social security number, and a visit to the Daily Grind, where he works, adds to his misery when Shirley, his employer, reveals that two men claiming to be cops came by and warned her about him, telling her that he has a history of violent and erratic behavior against his employers.
While all of the above takes place, Peter Parker and Mary Jane argue about whether to go back home to Portland or get to the bottom of the skeleton mystery. Meanwhile at the Multivex Corporation, the mystery man who has been harassing Dr. Seward Trainer is shown in more detail. He wears some kind of environmental suit that keeps his body functioning and he needs Seward to help him get back to his physical prime.
While out shopping, Peter and Mary Jane are attacked and dragged into an alley by a cybernetically enhanced mercenary squad known as Cell-12. Peter tries to convince them to let go of MJ, but to no avail (they do promise to not hurt her). The squad beats the hell out of Peter, until he falls to the ground. As they leave, they tell him to not poke is nose where it doesn’t belong. Meanwhile, Ben returns to his apartment and is shocked to discover it completely empty, the words "We Know Who You Are", written on the floor. Realizing that whoever did this to his apartment might want to lash out against his workplace, he rushes over there but arrives too late. The Daily Grind has been burned down to the ground.
In Spider-Man Volume 1 #8, the police try to implicate Ben Reilly into the Daily Grind fire, because of his history of lashing out at employers (which we all know is untrue). While this takes place, Peter Parker and Mary Jane discuss his recent beating at the hands of the Cell-12 squad.
Thinking that Jessica Carradine, his ex-girlfriend, is behind the recent misery in his life, Ben shows up at her apartment and warns her to stay out of his life. He swings off, as Spider-Man, and realizes that there is only one person he can talk to: Dr. Seward Trainer. Having tagged him with a spider-tracer earlier, he begins tracking him. He arrives at a location and is attacked by the Cell-12 squad. He disposes of them quickly and easily, and then comes face-to-face with their leader: the Hobgoblin (who now has many cybernetic enhancements on his costume). Having never faced the Hobgoblin before – this is Ben after all – he mistakenly refers to him as the "Green Goblin". During the ensuing battle, the Hobgoblin reveals that he has been orchestrating everything that has been happening to Peter Parker and Ben Reilly, as instructed by his employer. As he gets the upper hand on Spidey, the Hobgoblin is ordered to stop by none other than Seward Trainer. Spidey is shocked to realize that Trainer is involved and he cannot help but to watch helplessly – he is incapacitated by injury – as his friend walks away with the Hobgoblin. After a few minutes of gathering his strength, Spidey manages to get out of there, all the while thinking about this overwhelming development. He races to where Peter and Mary Jane are staying, enters their room, and collapses to the floor, waking them in the process.
Another issue worth noting is Spider-Man Unlimited #12. In it, J. Jonah Jameson wants forensic scientists to examine the bones of the skeleton to determine its identity. In order to examine the skeleton, Jameson has to find it first so he is offering a $100,000.00 reward to anyone who can locate the skeleton (as seen in Amazing Spider-Man #411). As a result of this, Spider-Man has had to deal with the likes of the Beetle, Shocker, Boomerang and the second Jack O’Lantern.
While Spider-Man deals with hordes of new super-villains trying to cash in on the reward, Peter Parker is forced by the Pro to dig up the skeleton, which Ben Reilly and him buried in a graveyard. Spider-Man makes his way to the graveyard to help Peter out but a welcoming committee made up of the police and reporters forces him and Peter to hand the skeleton over to them.
The forensic team reconstructs the face of the skeleton, only to reveal the face of Peter Parker. Since Peter took part in an earlier test to verify the authenticity of the imaging device, as per a request from J. Jonah Jameson, the scientists deduce that there is some kind of problem with their imaging system (they assume his earlier picture somehow got mixed up with this new one) and that, as such, the experiment is a failure.
In Spectacular Spider-Man #234, Ben Reilly is depressed about how he failed both as Spider-Man and as himself. As he talks to Peter and Mary Jane Parker about it, he confesses that he has come to the realization that the mastermind behind everything that has happened to them has to be Dr. Seward Trainer. Having a hard time wrestling with the idea that Trainer is involved, Ben, as Spider-Man, swings off into the night. Miles away, Trainer is having a heated argument with the mystery man introduced in Amazing Spider-Man #411 and his bodyguard, The Hobgoblin, about the fact that they had agreed that Ben Reilly would not get hurt. Trainer loses that round.
Ben goes to Jessica Carradine's apartment and apologizes to her for accusing her of being the mastermind being everything that has happened to him. He professes his love to her but then he screws up everything by asking her to burn the negatives of the pictures revealing that he is Spider-Man. Believing that he only apologized to her to get the pictures, she kicks him out of her apartment. While this takes place, Liz-Allan Osborn, current CEO of Osborn Industries, notices some irregularities while looking at the company’s quarterly financial report. She calls her brother, Mark Raxton, a.k.a. the Molten Man, to ask him if he knows anything about incredible amounts of money being funneled to a small research company called Multivex (where the mystery man and Trainer were arguing earlier); Raxton is clueless.
When Ben returns home, he finds out that Peter has gone to Multivex to get answers from Trainer. Ben immediately takes off after him.
Peter breaks into Multivex and makes his way through the building undetected, until he decides to take a detour and runs right into the arms of the Cell-12 squad. Thankfully, Ben, as Spider-Man, arrives on the scene and takes them all out. But then, the Hobgoblin shows up. Peter and Ben split up; Ben confronts the Hobgoblin while Peter takes off after Seward. Coincidently, Peter, Seward, Ben, and the Hobgoblin all end up on the same rooftop. Peter tackles Seward to the ground and is about to question him when he notices the Hobgoblin's glider heading towards a large fuel tank (Ben pushed the Hobgoblin off his glider during their fight). Peter launches himself after the glider and grabs hold of it. He tries to steer it to safety but loses control and is knocked off. Witnessing this, Ben abandons his battle with the Hobgoblin and rescues Peter. This distraction allows both the Hobgoblin and Trainer to disappear. At issue's end, Peter and Ben realize that the Hobgoblin and Trainer are but pawns to somebody else, which brings them right back to square one: who is behind everything and why.
In Sensational Spider-Man #5, Ben Reilly, as Spider-Man, tracks down the Financial Controller at Multivex, a woman named Trish Kowalski, and forces her to reveal that Osborn Industries if funding their company. Ben informs Peter Parker who, in turn, recaps what has happened between him and Harry Osborn and how Osborn Industries is now run by Liz Allan-Osborn and her brother Mark Raxton.
While the above takes place, Mark Raxton breaks into Multivex in search of clues about Osborn Industries' involvement with them. Meanwhile, Peter visits Liz to see if she knows anything about it. She denies being involved and vouches for Mark as well. Peter meets up with Ben and fills him in. They come to the conclusion that Raxton must be the one behind all their problems. Peter and Ben, as Spider-Man, go to Multivex and spot Raxton inside. Ben confronts him and accuses him of trying to ruin their lives; Raxton denies any wrongdoings. A battle naturally ensues, so Peter comes down to check things out. The fight between Spidey and Raxton takes a turn for the worse when they accidentally cause a minor explosion, which sends the two of them and Peter down to where Trainer is putting the finishing touches on his boss's suit.
In Amazing Spider-Man #412, the issue opens up with Spider-Man (i.e. Ben Reilly), Peter Parker, and Mark Raxton, surrounded by Multivex security team. While Spider-Man takes them on, Peter stands on the sidelines and Raxton confronts the mystery man, who seems to be orchestrating the whole thing. Raxton and the mystery man engage into a battle, during which it is revealed that the mystery man relies on his suit to survive because his body is dying and rotting away. It is also revealed that the mystery man is willing to do anything to be free, including working for the devil himself. The mystery man takes Raxton out and proceeds to engage Spider-Man into battle. During their battle, the mystery man reveals that Spidey has encountered him in the past, though his appearance was quite different than it is now. Spidey wonders who the mystery man is and shudders when he considers that it could be Harry Osborn, the second Green Goblin.
While this takes place, Peter continues to look for Dr. Seward Trainer but is interrupted in his search by a voice over the intercom announcing that the "game is over". At this point, it is revealed that Mary Jane was captured when she came over to Multivex to try and warn Peter and Ben. Peter surrenders and is captured.
While Spidey and the mystery man continue to battle each other, Seward calls out the mystery man, referring to him as Gaunt, and informs him that the regenerator is all set to begin the "rebirth" procedure. Gaunt proceeds to tease Spidey about the fact that his (and Trainer's) employer is another former acquaintance of his and then uses gas to knock him out before Spidey can react to this alarming news.
As Gaunt prepares for his rebirth, Peter, MJ, Spidey, and Raxton try to break free from their bonds. Spidey manages to expand his chest muscles and breaks free from his chains without drawing the guards' attention. During the ensuing battle, the regenerator is heavily damaged. Peter, MJ, Spidey and Raxton escape the lab unscathed, while Trainer stays behind to keep the regenerator from exploding before they can make it out of there. Believing Trainer to be dead, Ben/Spidey wonders if Trainer sacrificed himself for them by sabotaging the machine or if he was actually trying to save himself by saving the machine.
At issue's end, Gaunt accuses Seward of trying to sabotage the regenerator, which Seward strongly denies. Their argument is interrupted by another mysterious person who seems to be the real mastermind behind everything that has happened to Peter and Ben. Though little is revealed about his identity, clues that he has been manipulating events and people from the shadows for years seem to corroborate the fact that he is a former acquaintance of Peter's. He also vows to make Peter and Ben pay for what they did to him, at a time and place of his choosing. Who is this mysterious person?
In Spider-Man #69, Ben Reilly, as Spider-Man, tracks down and confronts the Hobgoblin. In the ensuing battle, the Hobgoblin carelessly confesses that it was he who attacked Peter Parker and burned the Daily Grind to the ground. He proceeds to laugh at Spidey, confident that no one will believe him if he tries to use that information. On cue, Peter and Ben Urich step out of the shadows, revealing that they were photographing and recording the whole conversation. Needless to say, the Hobgoblin stops laughing immediately. The following day, Ben's name is cleared so a celebration is in order. During said celebration, it is revealed that Peter and Mary Jane are moving back to New York City; Peter having accepted a job offer (as a photographer) from J. Jonah Jameson at the Daily Bugle. Throughout the issue, it is again emphasized that Trainer, Gaunt, and the Hobgoblin are all working for the same mysterious man, who still remains a mystery.
This issue picks up not long after.