During the intermission of a Broadway musical, Desiree Winthrop goes into the lobby to look for Ben Reilly, who excused himself from their date to make a phone call. She wonders where he could be until she looks out one of the windows and sees the streets are swarmed with bees that are attacking everything in sight. Not far away at the Institute of Seismoharmonic Research building has been taken over by the mutant bees controlled by the Swarm. The hive mind is attempting to use the devices within the facility to repair the damage to Swarm's psychic link to his bees and take over the world. Nearby, Spider-Man swings toward the building, he quickly makes note of the fact that Peter Parker must have fought this creature during the five years he Ben Reilly was gone. This is reinforced because of a genetic memory among the Swarm's bees that cause them to avoid him at all costs. This will make his job easier, the wall-crawler to give thanks to Peter Parker.

Meanwhile, in Forest Hills, Peter and his wife Mary Jane are redecorating one of the rooms in Aunt May's old house in preparation for their unborn child. Peter is on the ceiling painting when his spider-powers suddenly wear off causing him to fall to the ground. After making sure her husband is okay, Peter and Mary Jane decide to take a break to have a little romance. Back in the city, Spider-Man decides to push his theory to the limit by leaping into the mass of bees. This gamble pays off as the insects move out of the way allowing the web-slinger to gain access to the facility. He instantly recognizes the Institute of Seismoharmonic Research, having read about their work in an issue of Scientific American. Inside the building, he finds scientists hard at work on their new Harmonics Generator. The lead scientist explains that Swarm is forcing them to use the device to repair his damaged vibrational field that was damaged recently. However, not only are they going to restore his power, but boost it so the Swarm will take control of every beehive on the planet. When Spider-Man asks what the Swarm threatened to do if they didn't comply, and is immediately answered when the Swarm commands a group of his bees to fly into one of the scientist's mouth to choke him. After getting his message across the Swarm dissipates again so the scientists can continue their work.

Pulling the scientists aside, the wall-crawler points out that bee's fly by cutting through air currents by vibrating their wings, if they can disrupt this process they could incapacitate the bees. The scientists come up with a means to do it, but in order for it to work they need to get some equipment up onto the roof of the building. To this end, they trick the Swarm into thinking that they need to lug the heavy equipment onto the roof in order to restore the Swarm. The hybrid being falls for the ruse and allows them to bring the equipment up onto the roof, telling them that they can get Spider-Man to do all the heavy lifting for them. The Swarm doesn't realize that he is being tricked until Spider-Man and one of the scientists have set up the device on the roof of the building. Just as Swarm is about to attack, Spider-Man activates the vibration machine which once more severs the Swarm's mental connection to his bees. The process causes ripple on the psychic plane causing pain to those who are psi-sensitive, including Phoenix of the X-Men. The process also knocks all the bees out, allowing Spider-Man to locate and isolate the queen bee, the source of Swarm's link with the hive.

With the danger over, the scientists explain what happened to the press and are hailed as heroes. The scientists point out that Spider-Man is the real hero as it was his idea that helped them defeat the Swarm. This is heard by J. Jonah Jameson who is watching the report on television, causing him to audibly scoff at the assertion. While everyone is wondering where Spider-Man went, Ben Reilly has changed back to his civilian id

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