In 1987, Peter Parker followed Wolverine to Russia, who was on the trail of a friend working for the KGB. Realizing that the KGB would eventually kill his friend, Wolverine wanted to put her out of her misery. Peter tried to stop him, but accidentally killed the friend instead. Haunted by his actions, Peter fled home into the waiting arms of Mary Jane.
But WHAT IF…Peter never went home? WHAT IF…the Spider never came out of the cold?
A man by the name of Nebo is in S.H.I.E.L.D. custody. Nick Fury and the Black Widow stand before him. Fury is honored to be standing before this elusive man. He tells the Widow that Nebo trained an female operative named Alex. He makes killers. Nebo denies ever seeing her. Fury quickly points out that he already knows. Normally S.H.I.E.L.D. isn't concerned with his training since they usually end up in the C.I.A. That wasn't the case with Alex's sister, Charlemagne. She went on to work for the KGB. After she tired of that organization, she started killing them off. She hooked up with Wolverine and then Spider-Man got involved. Wolverine tried making Spider-Man go back home but Charlemagne tricked him into accidentally killing her, which is what she longed for. Spider-Man was messed up from causing her death. It's been a year and now Russian agents are dying again with claw marks and webbing left on their bodies. The story unfolds as to how Spider-Man was brought further into this world of espionage.
As Peter is about to board a plane back to New York, Logan shows him a picture of Alex. He figures helping her would be a way for Peter to redeem himself. The two of them set out to save Alex from some Russian agents. They soon find themselves faced with Fantasma and Crimson Dynamo. Spider-Man tries to stop Crimson Dynamo but his suit is too much. Finally Wolverine makes his way to his back and slices through the power cables of the suit. Not realizing that the suit is powered down, Spider-Man punches him and breaks his neck. Wolverine takes care of Fantasma with his claws. Spider-Man asks if everyone has to die. Wolverine says eventually yeah, but Alex doesn't have to right now.
After their escape, it seemed that Spider-Man figured if he could keep Alex alive, it would make up for everyone that had to die. He begins training with Nebo and soon expands the abilities of his spider-senses. Nebo learns that he can't even think of attacking Spider-Man without him realizing it. Peter and Alex started growing closer with all the time they spent together. Things didn't let up as the Russian operatives still wanted her dead.
S.H.I.E.L.D. was able to track money being sent back to Peter's Aunt. Nick asks where the rest of the money they made went. Nebo tells them that with Spider-Man and Wolverine's influence, a lot went to charities and some went to help mutants. The three of them began a mission of doing "good." Nick still doesn't see how all this has escalated the return of the Cold War. It turns out Spider-Man was tired of being on the defensive when it came to Alex's safety.
Fury tells Nebo he's lucky they grabbed him when they did. The next mission they were to go on has been revealed to be an ambush against them by the old Soviets. Inside a shack, Alex isn't finding much information from the computers there. Wolverine wonders where Nebo is. Spider-Man says he'll show up later. Wolverine starts getting anxious and Spider-Man asks them to get on the floor for a second. The place is under attack. Wolverine asks how they were able to get a drop on them without it tipping off Spider-Man's senses. Spider-Man now stands before a dude with two blades. Webbing is useless as he can easily slice them. Spider-Man surprises him by revealing a gun built into his web-shooters.
The fun's not over as they sense they are surrounded by snipers. Spider-Man tells the two of them to just stay alive for one more minute. Then a helicarrier arrives. S.H.I.E.L.D. orders the Russians to drop their weapons. A man tells Fury that this doesn't concern them. He tells Fury that they just want Alex dead for state security. Fury offers him something better and reveals that the man with them is the Rook. They decide to hand over Nebo to stop the Cold War. Fury says only if they let the three go. Wolverine is impressed that Peter set this all up. As Nebo is being taken away, he has one thing to say to Peter, he has now become his greatest student.
Fury decides to let them go too. He says he may even be stupid enough to hire them at some point in the future. Spider-Man hands a old beaten letter to MJ. He says it's too dangerous for him to even put an address on it. It turns out the letter is a goodbye to his old life.