Ex-convict Richard Deacon is transformed into THE FLY by Dr. Stillwell…in a plan conducted by J. Jonah Jameson! What will become of the Daily Bugle’s publisher when his plan backfires?
At the start of this annual, J. Jonah Jameson is in his office, angry because Spider-Man hasn't been captured after all of these years of his editorials, and the Daily Bugle's figures are starting to drop. As Robbie Robertson points out that the Daily Globe is making a comeback, due to them getting exclusive pictures of the White Tiger, J. Jonah Jameson still keeps raging. Peter Parker then comes in, and Jonah immediately yells at him for not arriving at the Bugle earlier. When he asks Peter why he hasn't taken any pictures of Spider-Man recently, Peter replies that Jonah had told him not to take any photos of Spider-Man attacking ordinary criminals, as it makes him look sympathetic. What's more, all of Spider-Man's foes that are worth photographing fighting Spider-Man - such as Shocker, Sandman, Vulture, and Scorpion- are all still in jail. Jonah then says that he's had a brilliant idea thanks to what Peter just said, and rushes out of the Daily Bugle.
Several hours later, at the waterfront the police are surrounding a building, where a kidnapper has two hostages inside, along with the rest of his gang. As the police wait outside for the kidnapper to contact them, Spider-Man arrives, and decides that he'd better help. He then uses his webbing to enter from the roof, knowing that the gang's attention will be on the police downstairs. Whilst the gang leader argues with his hostages for talking, they suddenly hear Spider-Man upstairs, although they don't know that it's him at the time, and one of the gangsters goes up to see what's there. Spider-Man easily knocks him out, but the noise from the fight alerts all of the gangsters, and they all start attacking Spider-Man. Spider-Man succeeds in taking out all of the gangsters except for the leader, a man called Rick Deacon.
Deacon still has one of his hostages, and threatens to kill her if Spider-Man attacks him. Spider-Man can only watch him walk out, not willing to risk the girl's life, but as soon as Deacon goes outside, Spider-Man grabs the girl out of Deacon's grasp with his webbing. With her safe, the police then open fire on Deacon before he can kill anyone, and Deacon's body falls into the river, with the police declaring him dead. Spider-Man then leaves, pleased with the work he's done. Further down the waterfront, J. Jonah Jameson is conversing with Dr. Harlan Stillwell, the brother of the scientist who created the Scorpion for J. Jonah Jameson. Although Harlan is hesitant, as the Scorpion became a menace to society, he eventually agrees to create a super hero for Jonah to get rid of Spider-Man, as he's low on money. Jonah makes a list of Spider-Man's powers, and how Harlan's creation has to rival each of them, and then leaves, telling Harlan to call him when he's done.
Harlan then goes over to a jar full of flies, and comments on how lucky he is that what Jonah wants him to do was exactly what his work involved. He then comments on all of a fly's abilities, saying that they would be able to fill out the requirements of Jonah's, although he still needs a volunteer. Rick Deacon, the kidnapper Spider-Man stopped earlier, then crawls in, saying that he'll do it. Since he's dying of the bullet wounds, he wants the powers, since it will heal him as well as complete the task Jonah wants Harlan to do. Harlan recognises Rick from a news report about the kidnapping, and is hesitant, until Rick threatens to kill him. Harlan reluctantly complies, and uses a machine on Rick that will bond the genetic coding of a fly onto him. Once he's done, Rick steps out of the machine, noticing that everything looks different, and that he can't feel the bullet wounds. He then declares that he's become a human fly.
Spider-Man meanwhile returns to the Daily Bugle to get some old shots of super villains, as he needs the money and it'll satisfy Jonah. In the Daily Bugle, Robbie notices that Jonah is tense, although Jonah denies it. A phone then rings, and Jonah is shocked by what the person on the other end of the line says to him. It turns out to be Harlan Stillwell, who tells Jonah that something has come up that they hadn't counted on, and that Jonah should head over there immediately. Jonah leaves just as Peter Parker arrives at the Daily Bugle, and arrives at Stillwell's lab shortly afterwards. Upon arriving, Jonah notices that it's eerily silent, and that there's no reply to him ringing the bell. As he steps into the main laboratory, he finds Stillwell dead, having been shot by Deacon.
Jonah's first thought is that he can't let anyone know that he was connected to Stillwell, as a scandal like that would ruin him. He then runs out of the building, hearing a loud buzzing, just like the flies that were in the lab. Rick Deacon, in a costume and calling himself the Fly, then appears before Jonah and knocks him out, saying that he'll use Jonah as bait to lure Spider-Man into his clutches. The Fly crashes into the Daily Bugle several minutes later, and gets rid of Robbie when he tries to attack him. The Fly then says that he's got Jonah kept hostage, and that he'll keep him until Spider-Man comes to him for a rematch. When Robbie asks what he wants with the Daily Bugle, the Fly says that he wants them to put out a notice telling Spider-Man to come to the Colosseum at midnight to fight him. The Fly then leaves, and Robbie decides that he'd better do as the Fly told him to.
Hours later, it's five minutes to midnight, and a large crowd of civilians and police are outside the Colosseum, waiting to see if Spider-Man will arrive to fight the Fly. A minute later, Spider-Man arrives at the Colosseum, just as he was expected to. He's immediately attacked by the Fly, and notices that the Fly is tougher than he thought. The Fly manages to tackle Spider-Man through a building wall, giving the police the opportunity to storm the building, looking for Jameson whilst Spider-Man is distracting the Fly. Spider-Man continuously taunts the Fly, and the Fly lashes out in a rage, seemingly knocking out Spider-Man. However, Spider-Man thinks to himself that he's purposely not fighting back against the Fly so that he can lead him and the police to where he's kept Jonah hostage.
The Fly reacts exactly as Spider-Man expected, and goes to Jonah, where he begins taunting him about how Spider-Man is going to be defeated, just as he wanted. Spider-Man realises that Jonah must have tried creating another villain to take him out, as he's done in the past. Spider-Man tries attacking the Fly from behind, but the Fly can see in all directions thanks to his eyes, and attacks Spider-Man. He then kicks Jonah off the girder that he's on, trying to kill him. Fortunately, Spider-Man saves Jonah's life with a giant web, which catches Jonah before he can be hurt. Spider-Man then uses his webbing to hold down the Fly's wings, and manages to use his skill and strength to knock out the Fly once and for all.
A few hours later, Peter hands Jonah a photo of the aftermath of the battle which he took, which has a photo of both the Fly and Jonah in webbing. Jonah angrily replies that he can't embarass himself on the front cover of his own newspaper, and so says that the public is sick of super villains, and wants more down-to-earth news (mirroring what he said to Peter at the start of the annual). Peter then says that Jonah should love the photos of purse snatchings that he's taken - all thirty of them.