- "So that's it. You just gonna run?"
"Feds were waiting for us. Now we're on Iron Man's radar? Yeah, I'm running. You should too."
"You know I can't do that."
"So now what?"
"Mason, can you get that high-altitude seal thing up and running in time?"
"Seriously? Yes. You will not regret this."
- ―Vulture, Shocker and Tinkerer
After the Attack on the Damage Control Truck, Toomes was still fuming over the failure to acquire any new materials. He took Phineas Mason up on his previous offer to build a high-altitude vacuum seal so they could pull off an airborne heist against the Stark Cargo Plane loading equipment from Avengers Tower. Toomes turned Mason down, asking if they still had enough technology to sell on the Staten Island Ferry in a few days which Mason confirmed. Toomes began muttering that it was all Spider-Man's fault and he would kill him for interfering with his business. Overhearing, Herman Schultz told Toomes to look at the television, which was broadcasting the Rescue at the Washington Monument, including Spider-Man saving Toomes' daughter, Liz.
After the Skirmish on the Staten Island Ferry between Spider-Man, the FBI was started to investigate which made Vulture and Shocker flew away, leaving Spider-Man to deal with the damaged ferry. After Iron Man showed up to repair the ferry and save the passengers, Schultz decided to leave the crew, as he feared their time was up now that they were on Iron Man's radar. However, Toomes asked Mason if he could get the high-altitude vacuum seal up and running in time and asked Schultz if he was ready to have one last score, which involved stealing from Tony Stark, and Schultz agreed to help.
Before the heist started he wanted to drop Liz and her date off at homecoming. He was initially not suspicious of Peter and would make attempts at having a conversation with him. It wasn't until his daughter started telling him on the ride to homecoming about Peter having an internship with Tony Stark and was friends with Spider-Man that Toomes grew suspicious. He asked Peter what it was like being saved by Spider-Man at the Washington Monument but Peter told him he wasn't there when Spider-Man showed up. This confirmed Toomes suspicions and once they got to homecoming he requested that he be left alone with Peter, under the guise of giving him the "Dad Talk'.
Toomes warns Peter Parker to stay out of his work or else he would kill him and everybody he'll ever loved. Peter refused to back down and, following a fight with the Shocker, he tracked Toomes back to his hideout with help from Ned Leeds and confronted him. Toomes tried to justify his actions to Spider-Man, explaining that everything he had done was to support his family and claiming that the wealthy and powerful care nothing for the common people like themselves. When Spider-Man refused to listen again, Toomes summoned his Exo-Suit to break the support beams around his lair, trapping Spider-Man under a pile of rubble and leaving him to suffocate.
With Parker seemingly being crushed to death, Toomes stepped outside and donned his Vulture Wings which had been upgraded by the Tinkerer. Looking out over New York City, the Vulture spied on Stark Tower and waited until the cargo plane filled with the Stark Industries weapons and the other Chitauri and Ultron technology was moved out so that he could steal it and sell all of the technology on the black market.
Vulture flew after and quickly caught up with and entered the last cargo plane leaving Stark Tower holding the equipment he planned to steal. Speaking to the Tinkerer during his flight, Vulture noted that the new Exo-Suit felt like it was dragging extra weight. Grabbing onto the side of the plane, Vulture cut himself inside using his gadgets and deployed a decoy drone to throw the plane's ground control, which Happy Hogan was monitoring. Entering the plane, Toomes discovered it was filled with even more than he could have hoped for, boxes of Chitauri weaponry, robotic parts of Ultron and well as various armors from the Iron Legion, all of which would be worth millions on the black market. Toomes began going through the boxes, throwing aside the one of Iron Man's old helmets to get to the Chitauri Guns. While attempting to alter the plane's course and marveling at the Avengers' equipment, Vulture discovered that Spider-Man had survived their previous encounter.
Furious, Vulture fought against Spider-Man outside the plane, using his claws on his suit to try and scratch at Spider-Man. During the battle, Vulture destroyed one of the engines in the process causing the plane to lose control. Fortunately, Spider-Man had successfully managed to use his Web-Shooters to redirect the craft away from New York City, crash-landing it on the beach at Coney Island.