However, Palpatine was secretly the architect of the entire conspiracy, as Dark Lord of the Sith Darth Sidious, and once alone with Fives and his guards, Palpatine told him the truth about what the chips were for–to force the clones to execute the Jedi–before ordering the guards to kill him. Fives fought back in self-defense, but when Shaak Ti burst into the room after hearing Palpatine screaming in apparent fear, it looked like he had attacked the Chancellor for no reason. Chased by the Togruta Jedi, Fives fled, his aggression and paranoia amplified by a drug Kaminoan scientist Nala Se had secretly administered to him. He eventually arranged a meeting with his superiors, Jedi General Anakin Skywalker and Clone Captain Rex, in a warehouse on Level 1325 so he could plead his case. However, Fives was killed by the Coruscant Guard when they tracked him there. With Skywalker and Rex disbelieving his claims due to the effects of the drug, Fives' death was covered up as the result of a parasite which had made his "inhibitor" chip break down, and the Jedi were none the wiser as to their intended demise.
During the Battle of Ringo Vinda, the clone trooper Tup began acting strangely and abruptly killed Jedi General Tiplar in the middle of battle, halting the Republic forces' advance. Unbeknownst to the Jedi or the other clones, the cause was a malfunction in Tup's behavioral modification biochip, which had been implanted in all of the clone troopers in order to ensure their obedience with carrying out Order 66. Tup was taken back to Kamino for investigation, as the Kaminoans, who knew of the chips but believed their purpose was as a safeguard against rogue Jedi, attempted to cover up their existence.
However, the ARC trooper Fives, Tup's best friend in the 501st Legion, was suspicious, and attempted to search for the truth, although Tup died shortly after his malfunctioning chip was removed. Fives, assisted by the droid AZI-3, discovered that the chips were implanted in all clones at an embryonic stage of development, and had his own chip removed. Eventually, after forcing Kaminoan doctor Nala Se to admit to the existence of the inhibitor chips, but only that they were meant to curb the clones' aggression, Fives convinced Jedi Master Shaak Ti to allow him to plead his case directly to Supreme Chancellor of the Republic Sheev Palpatine. However, Palpatine was secretly Darth Sidious, the Dark Lord of the Sith, and the architect of the entire conspiracy. Nala Se, after persuading Shaak Ti to allow her to accompany the Togruta Jedi and Fives to Coruscant, secretly drugged Fives with a compound that made him aggressive and paranoid on their approach to the city planet.
Upon the shuttle's arrival at the Grand Republic Medical Facility, Shaak Ti, Nala Se, and Fives were met by Mas Amedda and troopers of the Coruscant Guard, who escorted them inside to where Palpatine was waiting with his guards. Nala Se explained about Fives having removed his chip, and argued that this made Fives a danger to himself. Released from his restraints on Palpatine's orders, Fives defended himself, stating that given what had happened with Tup, the chips were clearly intended for something else. Eventually, Palpatine ordered Amedda, Shaak Ti and Nala Se out, claiming that Fives would probably feel more comfortable making his case with them absent, and stating that he was perfectly safe due to the presence of his guards.
Once only Palpatine, his loyal Coruscant Guard troopers and Fives were left inside the room, the Chancellor revealed the true purpose of the chips to the drugged Fives, and his involvement in the conspiracy, before ordering his guards to kill Fives, who counterattacked in his own defense. Shaak Ti and the others heard the Chancellor shouting in apparent fear from inside, and entered to see Fives grabbing a blaster and attempting to assassinate Palpatine, so the Jedi Master Force-pushed him away from the Chancellor. Fives then fled out of another doorway.
Aware that his pursuers were likely to disbelieve his claims about Palpatine attempting to kill him, Fives fled down a staircase, disregarding Shaak Ti's request for him to stop. She followed him as he ran through a room filled with doctors, patients and droids, shoving people roughly out of his way. However, when Shaak Ti ordered the blast doors closed, Fives was able to make it through the gap before the exit was sealed, to the Jedi Master's frustration.
Because he had attempted to assassinate the Supreme Chancellor, a manhunt was begun for Fives. Although the Jedi had not been officially asked to search for the rogue clone, the Jedi Council dispatched General Anakin Skywalker, Fives' commanding officer, to covertly search for him after Skywalker volunteered to look, along with Clone Captain Rex.
Fives eventually made it to the clone trooper bar 79's, where he saw fellow 501st member Kix and followed him into the refresher, asking him to contact Skywalker and Rex and giving him coordinates for a meeting place on Level 1325, before slipping out under the notice of Coruscant Guard troopers searching the place.
Skywalker and Rex arrived at an unoccupied warehouse only to be trapped in a ray shield by Fives, who attempted to explain the truth about Palpatine and the control chips, but could not articulate himself properly due to the drug administered by Nala Se, sounding insane. When Coruscant Guard troopers led by Commander Fox arrived in response to a sighting made by a probe droid, the paranoid ARC trooper went for one of Rex's blaster pistols and was shot dead by Fox.
With both Fives and Tup dead, the events were attributed by Palpatine to a parasite the clones had picked up on Ringo Vinda, with the Jedi unaware of the control chips that would eventually be their demise.
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