After Peter Parker discovered that his Spider-Man suit was being restricted by the Training Wheels Protocol, he had his best friend Ned Leeds disable it. Deciding to prove his worth to Tony Stark by locating the source of an illegal arms deal, the Karen A.I. was activated, much to his surprise. There, Karen congratulated him for completing his training and alerted him that he had many different web shooter combinations available. Still working out the improved suit, Parker was exposed to several different web styles in the heat of combat. Shortly after trying to intervene in Vulture's theft, Parker was ambushed by the Vulture himself. After a brief fight atop the moving vehicle, Vulture overpowered Parker and left him unconsciousness in the truck.
Parker later awoke in the Damage Control Deep Storage Vault in Washington, D.C.. Karen informed Parker that the only way out was through the sealed bay doors, which would not open until morning. With seemingly nothing to do but wait out the night, Parker discussed his suit's capabilities with his A.I, naming her "Karen". 
During the night Spider-Man was trapped in the Damage Control safehouse, it came to Karen's attention that a Chitauri power core Spider-Man happened to be holding was a dangerous explosive that detonates when exposed to enough radiation. Remembering that Ned Leeds had another lethal power core with him, Spider-Man immediately looked for ways out. Karen informed Peter that the bay doors could be opened if its security was overridden, but it would take most of the night to try every possible route. Roughly 200 trials into hacking the doors open, morning had come and Parker managed to open the doors. He requested Karen find the fastest possible route to Washington DC, where Leeds was.
Upon arriving, Karen informed Spider-Man that the elevator had been stopped due to a power surge from the core. Reacting quickly, Spider-Man scaled the length of the Washington Monument to attempt to access the elevator from the observation deck. After reaching the monument's peak, Spider-Man quickly became anxious about how high he had climbed, to which Karen advised caution, stating that he had neglected to restock a parachute in his suit, and wouldn't survive a fall from such a height without one.
As Spider-Man focused on the task at hand, Karen directed him to the southwest-facing window for access. As Spider-Man attempted to break through the glass, Karen kept him updated on the elevator's status, also informing him that at the rate he was going, he wouldn't break through in time to rescue his friends.
Upon the arrival of a Metropolitan Police Department helicopter, Karen quickly informed Peter that the elevator was about to fall due to the excess motion of the inhabitants as they tried to flee. With almost no time left, Spider-Man quickly jumped from the monument, using his web wings to gain height off of the helicopter's tail, and used his momentum to break through the glass, saving his classmates.
Following Aaron Davis' lead, Spider-Man sneaked into the ferry and went looking for Vulture. He learned that they were about to deal with a criminal named Mac Gargan to which Karen provided information about.
While Tony Stark was calling and speaking to Spider-Man, however, he could see that Randy Vale was preparing to hand over the Chitauri weapons to Gargan and the other criminals, so Spider-Man was forced to hang up on the annoyed Stark in order to focus on his targets before it was too late and Gargan got away. Spider-Man interrupted the deal and began fighting the crew and Gargan. Spider-Man fought against Herman Schultz who has gained possession of the Shocker's Gauntlet from Jackson Brice and then attempted to strike him with it. Spider-Man managed to defeat them, knocking Gargan overboard and trapping Schultz's arm but was then interrupted by FBI who began arresting everyone including Spider-Man who they mistook for Gargan's ally, much to his surprise as he tried to insist that he was not the criminal in this situation.
This distraction was all the Vulture needed to don his suit and began attacking Spider-Man and the FBI. While Spider-Man protected and saved the agents from the villain's attacks, Vulture freed his men and urged them to escape. Another fierce fight ensued as Vulture tried to kill Spider-Man with his advanced weaponry. Spider-Man countered by using his Web-Shooters advanced functions to even the odds, webbing Vulture to a car in an attempt to slow him down.
Vulture managed to free himself of Spider-Man's webs by cutting through them with his wings and continued attacking him. Eventually, the fight resulted in Vulture's Chitauri alien weapon malfunctioning. Spider-Man tried to webbed the weapon up only for Vulture to say he was dealing with things he did not understand. The weapon then exploded and cut the ferry in half. Vulture escaped as Spider-Man desperately tried to save the people inside the ferry.
Karen quickly calculated the strongest points of the ship and Spider-Man quickly went to work by webbing the strongest points together. Using his web-shooter and his own enhanced speed, Spider-Man seemingly managed to hold the ship together only to learn that his missed one spot and the ship starts collapsing. In desperation, Spider-Man webbed and painfully held both halves of the ship by himself in a herculean effort to save the ship.
Spider-Man noticed that the ship wasn't sinking anymore and it stopped being painful to hold the ship together. Iron Man revealed himself and has come to rescue the civilians. He quickly rebuilds the ship by reforging the cutlines. After that, he took Spider-Man away to have a private talk.