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Prior to Clu's takeover of the Grid in 1989, Clu developed a process to convert programs to his cause by filtering out their previous loyalties and directives and replacing them with loyalty to himself. Using secret facilities with the capacity to batch-repurpose large numbers of programs at once, he created the armies of Black Guards which were used to annex strategic portions of the Grid and to carry out the Purge.
The repurposing process at that stage, according to Dyson, was crude, leaving little of the victim's personality intact; for that reason he and Clu had determined to convince Tron to serve Clu by choice. This attempt, however, failed, though Tron was forced to watch his old security team be forcibly subjected to the change.
Various other attempts at mass repurposing techniques were developed over the cycles, including Keller's pathogenic code, but none worked well enough to come into common use; in the meantime, as a trade in stolen identity discs developed, the resulting strays were frequently turned in and secretly repurposed. Eventually Clu perfected the original process enough to leave some repurposed programs, such as Cutler, with enough of their original personalities to fool programs who had known them before into thinking they were still free. He commissioned a specialized mobile repurposing facility, carried in a giant recognizer, and dispatched Cutler, who retained all his old memories but had become a fanatical loyalist convinced that Clu had "shown him the light," to Argon City to offer Tron healing from his ostensibly irreparable wounds - to be followed by the insertion of the repurposing code. Tron, whose injuries had progressed beyond sustainability, was forced to take the offer, but explained to Beck that before repurposing could begin, he would have to be wiped clean of foreign code; if Beck could interrupt the process before the repurposing code could reach him, he could reap the benefits of the healing process without being compromised.
Upon reaching Cutler's recognizer, Tron entered the repurposing tube and his disc detached from his back and rose into the air. He raised his hands, his eyes white and blank; the corruption that had caused his injuries was removed in a stream of blue code rising from the center of his forehead up through his disc. When the blue code had stopped flowing, the device that had taken it switched to a different contact point and a stream of red code descended through the center of the disc toward Tron's forehead. However, the Renegade arrived and threw a Black Guard through the tube, shattering it and allowing Tron, fully restored, to escape.
In the subsequent battle, Beck revealed his identity to Cutler, causing a shock severe enough to briefly undo Cutler's repurposing. Cutler, confused and disoriented, painfully struggled to regain his freedom, and his circuits flickered from red to white and back again; but the code proved to be too strong and locked in irrevocably, forcing Beck to drop him and the light grenade he'd been holding over the side of the recognizer, where he derezzed.
During the following cycles, Clu did succeed in capturing and repurposing Tron, leaving him a masked, hunched figure showing little of his former personality. The repurposing process became known as rectification, and it became standard procedure to sentence dissidents, rebels and strays captured in Tron City either to rectification or to the Games. Programs slated to be repurposed were carried by Solar Sailer to the rectifier in silent, dormant batches, there to be herded into orange-hued repurposing chambers and emerge as identical sentries. By 2010, the unrectified population of Tron City had fallen drastically, and rumors of programs disappearing off the streets were connected by Zuse to Clu's "private initiative" to invade the real world with his army of recitified programs.
Tron's rectification came undone when he, having acted for many cycles as Clu's most loyal and deadly soldier, flew his light jet over the jet carrying Kevin Flynn, who was attempting to escape the Grid. The sight of Flynn's face looking back up at him allowed him to experience flashbacks to Clu's coup, distracting him from the chase. Afterward, instead of shooting down the escaping jet when Clu ordered him to, he uttered his old signature line - "I fight for the Users", - and flew his jet directly into Clu's, derezzing both jets and leaving him to plunge into the Sea of Simulation. As he sank into its depths, his red circuits flickered off and then on again, restored to their original white.