Clone crisis! After the mysterious death of his friend Tup, ARC Trooper Fives embarked on an investigation which led to the discovery of a hidden chip which is placed inside clone troopers when they were still embryos. The Kaminoan scientist, Nala Se, claims the chip is harmless, and is meant to restrain the clones from violent, unpredictable action. Fives claims otherwise and has convinced Jedi Master Shaak Ti to allow him to plead his case directly to Supreme Chancellor Palpatine on Coruscant....

A Republic attack shuttle approaches Coruscant. Aboard it are Nala Se, Shaak Ti, and Fives, who lies prone, restrained to a table. Nala Se surreptitiously injects Fives with an unknown substance. Fives falls unconscious as the shuttle settles on the landing platform of the towering Grand Republic Medical Facility. Mas Amedda escorts the new arrivals into the heart of the facility, where Chancellor Palpatine awaits flanked by his red-robed guards.

Fives awakens before the Chancellor, who is most intrigued by his story of inhibitor chips. Shaak Ti hands Palpatine the harvested samples -- Fives' healthy chip and Tup's degraded one. Fives explains his belief that the chips are an enemy plot. Palpatine asks Shaak Ti and Nala Se to leave the room, so that Fives can better explain his suspicions without their observation.

With reservation, Shaak Ti and Nala Se depart. Within moments, there is the sound of a scuffle inside. Shaak Ti races inside to find the guard troopers knocked to the ground and Fives standing over the Chancellor with a blaster rifle. Shaak Ti uses the Force to knock Fives over, and races to Palpatine's side. A breathless Palpatine explains that Fives tried to kill him.

Fives runs out of the chamber into the corridor. Palpatine concludes that Nala Se was correct -- Fives has gone mad without his inhibitor chip. He returns the inhibitor chip samples to the Kaminoan scientist. Fives dashes out of the hospital, outrunning and outmaneuvering a pursuing Shaak Ti and shocktroopers.

In the war room of the Jedi Temple, Master Yoda, Shaak Ti, Mace Windu, and Plo Koon examine a holographic image from Fives' escape. Shaak Ti briefs her fellow Jedi, and Mace explains that the Chancellor has been safely transported to his Senate quarters, and that the clone and security forces on Coruscant have been mobilized for a manhunt.

Anakin finds it odd that the Jedi have not been involved. He is determined to find the truth behind Fives' shocking behavior. Skywalker feels that since Fives was a member of the 501st, he might trust Anakin and Clone Captain Rex.

On the streets of Coruscant, Fives continues to shake off whatever drug Nala Se had injected in him. He boards a hover taxi and directs the driver to 79's, a sort of sports bar for clones. After stiffing his cab fare, Fives slips past several drunk, rowdy clones and enters the bar. He spots Jesse and Kix inside. Fives follows Kix into the refresher, where he reveals his identity.

Kix is surprised to see Fives -- word has spread that Fives tried to assassinate the Chancellor and that he is infected with the virus that killed Tup. Fives tells Kix that he's been framed and that there's a huge conspiracy afoot -- he must talk to General Skywalker or Rex. Kix promises to contact Rex, so Fives leaves a set of coordinates for a rendezvous before slipping back into the dark.

Fives sneaks past shock troopers checking clone IDs and steals a speeder bike to disappear into the lower levels of Coruscant. A floating observation droid watches his departure with its unblinking photoreceptor.

Fives pilots the speeder bike through one of the yawning portals that cuts into the Coruscant underworld. He lands at a portal warehouse on Level 1325, groggy from the drug that Nala Se has injected him with. An observation droid confirms his identity, recognizing his distinct markings. The droid alerts Palpatine's shocktroopers with Fives' location.

A police gunship lands at the portal warehouse and Anakin and Rex emerge, following the lead Kix gave them. Inside the warehouse, Anakin ignites his lightsaber to illuminate the dense darkness, and he calls out to Fives. Fives asks Anakin and Rex to put down their weapons. They comply, trusting their friend and fellow soldier. Fives lures Rex and Anakin into a force shield generator and traps them inside.

Fives insists he had no choice. He explains that he has uncovered a massive conspiracy, and that the clones are engineered with organic chips that allow someone else to control them, to even make them capable of killing the Jedi. Fives desperately realizes he has no evidence. The drug and desperation make Fives seem all the more frantic and unhinged. Fives insists the Chancellor is in on it, and that Palpatine told him as much in the medical facility.

Just then Clone Commander Fox and his troops burst in, demanding that Fives stand down. Desperate, Fives grabs one of Rex's blaster pistols, but Fox opens fire, killing Fives with a shot through his heart. The shocktroopers collapse the shield around Anakin and Rex, and Rex rushes to Fives. With his dying words, Fives warns Rex that this conspiracy is bigger than anything anyone could have imagined.

Back at Palpatine's office, the Supreme Chancellor expresses his dismay to Yoda, Mace Windu, Shaak Ti, and Anakin at learning that Fives has died. He informs them that his own personal doctors have examined both Tup and Fives, and discovered something that Nala Se missed: a parasitic infection native to Ringo Vinda. Fives and Tup were most likely infected from a shared source, like a canteen of water, Palpatine explains. As a precaution, a vaccine has been prepared for the soldiers of the clone army.

On Serenno, Lord Tyranus communicates with Nala Se, confirming that he has received the inhibitor chip samples she has forwarded. Tyranus contacts Darth Sidious, assuring his master that the Sith plot has gone undiscovered.