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.

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.

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.

Ecstatic about this great news, Ben goes out swinging as Spider-Man and runs into the Lizard, after being alerted of his presence along the waterfront. In the ensuing battle, the Lizard takes off towards the hospital where Peter is recovering. Ben follows him and the two of them continue their battle on the hospital rooftop. Inside the hospital, Peter Parker is visited by Dr. Curt Connors when they become aware of Ben and the Lizard fighting each other. Apparently frightened, Dr. Connors takes off without explanation. Wanting to find out if his spider-like powers have returned, Peter makes his way to the rooftop to help his "brother". Though he makes it to the rooftop and helps Ben to a certain extent, Peter is accidentally pushed off the ledge of the building and Ben is forced to abandon his battle with the Lizard to save him. At issue's end, as they regain their strength, Peter informs Ben that the Lizard he was fighting was not Dr. Connors since he was just with him minutes earlier.

The new Lizard shows up at Dr. Connor's house and attacks its creator and his son, Billy, who was in the process of being punished for coming home past curfew. Father and son manage to lock themselves inside the nearby lab, praying that the door will hold. Thankfully, Spider-Man (a.k.a. Ben Reilly), who heard about the new Lizard on the news and traveled to Florida to help his friend, arrives on the scene and confronts the new Lizard. In the ensuing battle, the new Lizard is sent flying into thick bushes, where a loud snapping noise is heard. When Spidey goes to investigate, he comes face-to-face with the original Lizard, holding the neck-broken new Lizard in his scaly hands.

When Ben awakens the next morning, he finds himself back in his apartment, his arm throbbing from an antidote Kaine injected while he was passed out. Ben finds the real Janine, sleeping in his bed. He wakes her up and hugs her for what seems like an eternity. Janine tells Ben that they should move away from everyone and everything. Just then, Ben's spider-sense kicks in, warning him of danger. Believing Kaine to be back, Ben grabs hold of Janine and the two of them race out the door, only to find the police waiting for them. More specifically, they are waiting for Janine, who is under arrest for the murder of her father.

As they continue thinking about leaving, Janine explains how Kaine, all those years ago, kidnapped her, when she and Ben were in Santa Cruz, and forced her to leave and never come back by threatening to reveal her past. Kaine’s goal was to make Ben think she was dead, that she had been ripped away from him, just as Gwen Stacy head been years earlier. As if on cue, Kaine shows up. Totally infuriated, Ben starts screaming and kicking at Kaine with everything he has. As far as Ben is concerned, Kaine is not just a clone – he is the darkness in his own soul. Before things get out of hands, Janine manages to calm Ben down. Kaine taunts Ben by telling him that he has already become just like him and vice versa. He then mentions that it's all over and before Ben or Janine can react, the Daily Grind explodes.

Now alone, Ben thinks about everything that has happened, and believes Janine will find her way and that she will be vindicated in the end. He also decides that he will try his best to help Kaine find inner peace. Perhaps telling the judge and prosecutors about the horrible circumstances that made Kaine the way he is will help him attain that goal. In a sense, his greatest enemy would become his greatest advocate. At issue's end, Ben, as Spider-Man, looks down from the rooftop, as Janine is taken into custody. Ben comments that as long as he lives, he will love her and he will always be watching over her, both as Ben Reilly and as Spider-Man.