Mary Jane Watson wakes up to find a conflicted Peter Parker watching the news regarding the Super-human Registration act. The news report goes on, saying that both the Fantastic Four and Stark Enterprises have and will make billions of dollars off of security regarding.
Peter travels over to Stark towers to find a tired Stark working away at a computer. Peter interrupts Stark, asking if he could see the Negative Zone, the holding area for super-humans.
Peter is alarmed to find out that the holding area is the Negative zone, and the inhumanity of the prison alarms him. People are confined to small cubic cells that combat the super-human's powers, from being fire resistant to emitting counter-frequency.
As Tony finishes up the tour of the holding area, Peter begrudgingly remarks that it's barely satisfactory, -- for a temporary holding area. Tony replies, "This isn't temporary. This isn't interim. This is permanent. Get with the program."
Peter is aghast that these people are stuck in the Negative Zone for life simply because they refuse to sign the Super-human Registration Act. Tony draws a parallel to putting an atomic bomb on parole, and that extremes had to be implemented in order to contain the type of people they were dealing with. Iron Man is also quick to bring up that the Negative Zone is outside the jurisdiction of any country or any agency found on Earth, so the prisoners were denied the right to a trial.
As the two leave the gateway to the Negative Zone, Peter sees Reed Richards and asks to talk to him in private (away from Iron-Man). Iron Man leaves (although it is revealed in a different comic, he overhears the entire conversation), and Peter asks why Reed is siding with the SHRA. Reed recalls the story of his uncle, who was essentially condemned of being a communist (which he wasn't) simply because he stood out. Reed says that the loss of his uncle devastated him, and Reed couldn't bear to cause that sort of devastation to those he held close to him.
Iron-Man picks up Peter, and the two start making it to the airport. Iron-Man says Peter needs to go to Los Angeles, to cool off, saying Peter had become to involved in the SHRA, and they needed him in LA.
On the next page, Peter sneaks back into his house and quietly wakes up both Aunt May, and Mary Jane. He tells the two that they need to leave, saying he's made a terrible mistake which he has to rectify, and they can't be around.
Distant 'booms' rattle the building, and Peter tells the two to hurry. He quickly let's his suit materialize and starts to run away from both the booming and his family.
Iron-Man crashes through the wall, dive tackling Spider-Man. Spider-Man sarcastically remarks, "I thought you said you were going out for the night, Dad"
To which Iron Man replies, "And I thought you knew which side you were on"