One day, high school senior Marcus Yallow is skipping school in San Francisco, California, with three of his friends: Vanessa "Van" Pak, Jose-Luis "Jolu" Torrez, and Darryl Glover. A girl in bright pink almost reports him as truant, but she is stopped short when terrorists blow up the Bay Bridge.
In the ensuing chaos, everybody floods into the BART stations, including Marcus and his friends, but they soon exit because of the craziness and intense press of bodies. After they get out, Marcus finds that Darryl has been stabbed. He tries to flag down one of the many emergency vehicles that are speeding by, but ends up stopping a Hummer full of guys with guns.
These guys capture the four of them and transport them first by car and then for a short time on a boat before locking the four of them in cells. In the following week, Marcus and his friends and brutally interrogated by a woman who works for the DHS who Marcus nicknames "Severe Haircut Lady." For the most part, they try to obtain the usernames and passwords for Marcus's various devices and accounts. In the end, they do, but do anything about it, except tell him that they had enough information to put him way for a long time.
About a week after they were captured, Marcus, Van, and Jolu are released, but Darryl is nowhere to be found.
The three of them head to their respective homes. Marcus's parents, Lillian and Drew Yallow, are happy to see him, revealing that they thought he was dead. The next day, though, Marcus is sent to school, supposed to act like nothing ever happened.
Throughout the day, Marcus finds that everything has changed in their city. On the street, people are being stopped for "unusual activity," and at school, there are classrooms in every classroom. He even finds a bug that was placed in his computer. Marcus hates the added security, and he vows to take down the DHS for this and for whatever they did to Darryl.
Marcus head home and uses his immense amount of skill with technology and some free Xboxes that were given away the previous year to create an internet network that is private from the DHS's prying eyes. He spreads it around at school, and within a couple of weeks, thousands of people across the city are using it and calling it "Xnet." Then, inspired by Van, Marcus and Jolu figure out a way to change the amount of encrypted traffic that everybody on the Xnet is using, changing it from about 5 percent per person to about 95 percent. This is all done to confuse the people from the DHS that are watching and monitoring.
Because of this little stunt, Van is angry at Marcus and Jolu. She thinks that they are being stupid and reckless, and says that she can't watch them destroy themselves trying to fight against an organization that is far too large to be taken down by a couple of teenagers.
The next day, Marcus posts how to make an arphid, or RFID, cloner on the Xnet under his new handle, "M1k3y." An RFID is a radio frequency ID tag. Many things have a radio frequency ID, some of them being IDs and credit cards. An RFID cloner switches the tag of one thing with another over and over again. Total chaos ensues, and Marcus and his father clash over privacy and security.
Marcus and Jolu begin to worry that Xnet might be infiltrated by a DHS spy, so they plan a party at a place called "Sutro Baths" to create a web of trust. Only people who are trusted by one of the two of them are invited. It is at this party that Marcus meets Ange, one of Jolu's friends who is a girl who is super interested in privacy and, according to Marcus, is attractive in an unconventional sort of way. It is apparent that she is very interested in Marcus.
As the party comes to a close, Jolu tells Marcus that he is going to stop helping with things because he is afraid of getting caught. Marcus thanks Jolu and expresses the team loss that Jolu leaving is going to be, but doesn't protest.
In the days following the party, Marcus and Ange flirt, and Ange eventually invites Marcus to an illegal open air concert in Dolores Park, with the theme being "don't trust anybody over 25." There are some really good bands, including The Speedwhores, headed by Trudy Doo. Trudy runs the ISP at Pigslpeen, where Jolu works, and is also very concerned with privacy.
Marcus and Ange eventually head across the street and begin to make out, but the police, across the street, shut down the concert and drop pepper spay on the entire crowd. Due to their distance from the park, Marcus and Ange escape without any conflict.
The next day, the newspapers are calling it a "youth riot." Ange tells Marcus to host a press conference on Xnet to tell his side of the story. This online press conference is well attended by many in-game avatars representing real life journalists and reporters, but this group doesn't seem to get why this group of teenagers are so obsessed with privacy.
Back at school, Marcus's favorite teacher, Ms. Galvez, who taught about things like Freedom Riders and Women's Suffrage, has been replaced by a pro-government mouthpiece named Mrs. Andersen, whom everybody hates.
After Marcus gets out of school, he bumps into a guy named Zeb on his way home. When he gets home, he finds that Zeb slipped him a note outlining that he was imprisoned with Darryl on Treasure Island, where the DHS has been conducting their illegal interrogations. It proves that Darryl is still alive. The note inspires Marcus to tell his parents about the interrogations that he was put through, along with Darryl's dad and a woman called Barbra Stratford, who is an investigative reporter. Barbra starts to investigate the story of the interrogations that have been being done by the DHS on Treasure Island.
Marcus finds that his web of trust has been breached by a spy from the DHS when this spy, named Masha, contacts him and tells him that she is tired of spying on people. She says that she wants out, and that she'll help Marcus disappear too, because the DHS is getting close to figuring out who he is. He just needs to make an Xnet distraction as cover.
For this distraction, Marcus organizes VampMobm which is where a bunch of people dress up as vampires and gather in one location to play a big Live Action Role Playing (LARP) game. Marcus starts to escape with Masha, but while escaping, Marcus realizes that he has to stay and fight. He traps Masha in a truck and runs away from her, and with the help of some fellow Xnetters reconnects with Zeb. Van comes back and helps get information for Barbra. Everything seems to be working out perfectly.
But then Marcus gets captured by the DHS. He is taken back to the secret prison and waterboarded by the woman Marcus calls "Severe Haircut Lady" and a few others. Fortunately, Marcus is saved by a police raid headed by Barbra Stratford. After he is rescued, he finds Darryl still locked away in a maximum security cell at the end of a hallway.
In the end, Marcus gets arrested, but is ultimately only convicted of stealing a phone. Even though Marcus has done his work, though, the fight for American rights continues on.
