Spider-Man finds himself caught in the middle of a battle between X-Factor and the covert government group called Shadowforce. Spider-Man does NOT have time for this... because he has to go after Mirrorshade, the maniac making his way back to Manhattan to kill Flash Thompson after picking up one of Spider-Man's stray thoughts. When Spider-Man explains the situation, the members of X-Factor offer to hold back the rest of Shadowforce, allowing the wall-crawler to go after the errant agent. Spider-Man feels uneasy about leaving X-Factor to deal with Shadowforce alone, but agrees.

As Spider-Man exits the scene, General Sharpe is informed that Spider-Man is leaving with a copy of his secret files. He orders Shadowforce to ignore X-Factor and go after Spider-Man instead. Shadowforce manages to execute a maneuver that allows them to escape. As X-Factor recover from battle, they are confronted by the General, who tries to pull rank by ordering them to cease any further action in the matter. Havok is furious over these orders, and tells his team to hit the road.

By now, Spider-Man has managed to catch up to Mirrorshade. Unfortunately, stopping him is more difficult than catching him. After getting cold-cocked by Mirrorshade, Spider-Man is unable to prevent him from getting away. Since there are no buildings to swing from, Spider-Man tags his foe with a spider-tracer.

Spider-Man follows the signal to Union Station, where he manages to catch the next train back to New York City. Stealing a trench coat, Spidey ditches his costume so he can search for Mirrorshade in secret, as the rest of Shadowforce arrives by train. Meanwhile, the members of X-Factor are heading back to New York City themselves, as they know that's where Spider-Man is headed. Additionally, General Sharpe learns that the Daily Bugle has published a front-page story about his covert operations. He assures his subordinates that he will handle this situation.

Back aboard the train to New York City, Peter decides to buy himself some time. He borrows another passenger's cell phone and tries to call Flash. Instead, he gets Flash's voice mail, forcing him to leave him a message telling Thompson to meet him at the old Coffee Bean location. Finishing his call, Peter recalls how he failed to save his Uncle Ben and Gwen Stacy, and vows not to fail Flash.

By now, the Shadowforce member known as Firefight has become impatient, and opens fire in order to draw out Spider-Man. The ploy works, and forces Peter to lure Shadowforce up to the top of the train. In order to prevent the passengers from being hurt, Spider-Man detaches the other passenger cars and tosses the conductor onto a web cushion. With all the innocents safely away, Spider-Man is able to face Shadowforce.

He doesn't have to fight them alone, as X-Factor finally arrives on the scene. The situation changes suddenly when the battle rages beyond the range of the devices that keep Shadowforce in check. Finally free of the government's control, the villains disable X-Factor's ship and separate the last passenger car from the engine, leaving X-Factor and Spider-Man stranded as they escape.

Meanwhile, Mirrorshade arrives in Manhattan and finds Flash Thompson working at the Boy's Club. Spying his target, Mirrorshade prepares to kill Flash Thompson...

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