It was five years since Sam Flynn first got digitized and he has since recruited 14 other users, designed countless tools and vehicles, restored the ISO race, and created another Codified Likeness Utility – Clu 3. He was designed to promote peace between Basics and ISOs. Sadly, he did his job far too well. The ISOs and Basics decided that the users should join them in the grid, and designed a bomb capable of bringing the entire universe into the grid. Fortunately, the 15 Users managed to steal the trigger before they used it. Flynn managed to get the trigger from Quorra and some basics before they were ambushed by Elite Guards and derezzed. Flynn ran for his life, carrying the trigger…

"Damn it Will! Where are you…" Flynn rezzed in a lighttrike, a new, more advanced version of the lightcycle with a photon beam and a 'fishbowl' windscreen for tactical planning, and sped away, closely followed by three Elite Guards on lightcycles. Flynn fired his beam at a rock formation and derezzed one Guard. Suddenly, A familiar face sped up and derezzed the other two guards. "Flynn! Where's Quorra?" Will asked as he raced up to Flynn. "She's dead. Remember those friends of ours? They derezzed her and the other User-supporting programs." Will grimaced, and they entered the dark passageway of the expanded safe house that the elder Flynn had stayed in so many cycles ago. "So it's just the ten of us against the entire grid? Typical." Flynn couldn't help but smile at his best friend's remark. It was true; they once fought against Clu 2, Kevin Flynn's evil doppelganger.

Will was also right on another fact: there were only ten of them left. The other five had been hunted down and went missing one by one since Clu 3 hatched his plan. The first, Hope, went missing during the initial escape from Clu's base. The second, Jack had been lost while gaining intelligence on Clu's activity. The third, Ashley, went missing while searching for water and food. The fourth, Aiden, was sent up to the real world to ask for assistance and digitize food into the grid to supplement their limited food supplies. No assistance had yet been given. The fifth, Evangelyn, was Will's younger sister, and was the cause for his now-frequent bouts of depression. You see, Evangelyn, a.k.a. Eve, was Will's last living family member. His mother had died four years after Flynn and Will met, and his father had died when Will was two. No other family members existed. Their family had always had only one child for 60 generations, and Will's family broke the tradition, giving birth to Eve. Ever since she went missing, Will had very violent mood swings.

It pained Flynn to see Will like this, so he had three spies get info on her whereabouts. All he got was pictures of a female Elite Guard whose circuitry looked strikingly like Eve's, but the helmet was of the wrong design and she used a lightcycle and not a lighttrike. Among the photos were also pictures of other Elite guards that looked very familiar, but Flynn still couldn't put his finger on where he saw them.

Will looked out at the view. Jennifer, another surviving user, walked up to him and asked, "Nice view, huh?" Will turned and looked and said, "You know that's not why I stand here every day." Jennifer put a hand on his shoulder and said, "She's out there Will. Somewhere." Will sighed and exclaimed, "Maybe we should just let them detonate the bomb! Then Eve would still be here and Aiden and Jack and Hope and Ashley would all be here with us." Jennifer sighed and said, "Some people wouldn't make it. And besides, they can't know about cyberspace. It'll change the way things are run, and Clu would have total dominion over everything." Will sighed and went back inside.

[IN TRON CITY] Clu asked his technicians, "When will the Secondary Trigger be certified for safe use?" Frank-1, the lead technician, replied, "Another sixteen cycles Clu, only another sixte-" He only got that far before Clu derezzed him in fury. "Two cycles is too long! We need it to go off in another three cycles or we'll miss our chance to detonate it!" The remaining technicians stammered, "But the bomb may blow the entire universe to pieces if we do not certify it!" Clu calmed down and replied, "I'm willing to take the risk." The technicians gulped and gave Clu the device. Clu called for the Light Runner to take him to the bomb silo. "Soon, the bomb will go off, and the users will submit," thought Clu, "Or face death in the game grids."