By the end of the pilot, Callie suspects that the crash that killed her father and put her in a wheelchair was caused by hackers. Now she's determined to find out more.
Episode two begins as Callie finally views the logs of her crash, studying a recreation of the worst moments of her life. But there's something wrong - if the reality had been as the logs show, the crash would have been different than Callie remembers. Someone tampered with the logs, and Callie has the first evidence that hackers caused the crash.
After one particularly difficult hack, Callie finally encounters the Bright Man at Gibson's. Unknown to Callie, the Bright Man is the hacker who caused the crash. And for the first time, the two talk. But Callie is disturbed: the Bright Man knows things about Callie he shouldn't know, things about Callie's childhood. How could that be?
Callie starts to suspect Radu Tepes. After all, he was a longtime friend of Quincy Grant. He knew Callie as a child.
But the Bright Man isn't the only person Callie meets in Cyberspace. She also befriends a hacker who goes by the name Wallaby. And Wallaby gives Callie more reason to suspect Radu. There's a secret part of the Cyber Lab's network, the Annexe, that only lab members with security clearances can access. And Callie is not one of them.
Callie continues poring over the crash logs. But she makes no headway until, home from college, she finds the toaster acting weird. Her mother tells her that Quincy would modify the firmware for any device in their home and enhance it. Callie realizes that if Quincy modified the toaster, he probably modified his car. She breaks into his computer (not an easy task - Quincy Grant was a computer security rockstar) and finds the updated code. Updates that, among other things, created more detailed logs, logs kept in Quincy's private data warehouse.
Callie hacks into the warehouse. But she wakes with no memory of the hacking session - something killed her avatar in Cyberspace, leaving no trace. After a series of attempts, each leaving her with no knowledge of her struggle, she finally triumphs and discovers that all along she was battling the Bright Man.
Now she has the full record of what happened during the crash. And now she learns that the Bright Man was the killer. The only thing she doesn't know is who is behind the avatar.
Meanwhile, Wallaby tells her about a secret group of hackers that he works with. The Twilight Coalition fights cyber-spying by governments worldwide. And the Annexe is part of the government's efforts to track American citizens. Wallaby asks Callie to hack into the Annexe and let the Twilight Coalition in to sabotage the NSA's surveillance.
Callie resists, though she becomes romantic with Wallaby, even cyber-physical, though they've never met in the real world. But Callie's suspicions of Radu grow, and she breaks into his computer and makes a terrible discovery. In a virtual room where Radu keeps his avatars - a collection like Batman's set of costumes - Callie finds the avatar of the Bright Man. She now knows that Radu is the bright man. He killed her father: she just doesn't know why. But that's enough for her. She breaks into the Annexe and lets in the Twilight Coalition.
She encounters Radu and confronts him. But things are not as they seem. Sure, Radu had the Bright Man avatar. But that's because he still has Quincy Grant's collection of avatars and the Bright Man was among them. And the Twilight Coalition is not a group of cyber-vigilantes. It's an evil conspiracy, and by letting them into the Annexe and, by extension, into the NSA, Callie has allowed them one step closer to world domination.
In the last scene of the season, the Bright Man walks into the now hacked Annexe. On seeing a picture of Quincy Grant, founder of the lab, the Bright Man stops. For the first time, he removes his blank face. Staring out we see Quincy Grant.