Cause of death unknown! Kaminoan doctor Nala Se was unable to find a cause for an illness in clone trooper Tup. In a desperate attempt to save his friend's life, Fives located and removed a tumor from Tup's brain with the help of medical droid AZI-3. Immediately following the procedure, Tup died and Fives was placed under arrest. Now the tumor is the only hope to finding answers for Tup's mysterious illness....

Fives sits under guard in a Kaminoan observation room. Shaak Ti informs him that the tumor and all intelligence regarding the matter of Tup's illness are being sent to the Grand Republic Medical Facility on Coruscant. Fives wants to accompany the sample, but Nala Se and Shaak Ti deny him this chance. Fives is due for one more examination before being returned to the 501st.

Nala Se blames Fives for Tup's death, an accusation that goads Fives into anger, but Shaak Ti orders him to stand down. She feels Nala Se is out of order. Shaak Ti commands that all samples be prepared for transport to the Jedi Temple. Despite Nala Se's protests, Shaak Ti intends to bring the samples first to the Jedi before handing them over to the Chancellor for further examination. As Fives is marched out of the observation room, he witnesses Nala Se's medical droid switch the sample boxes.

Fives is marched down a corridor by clone troopers and a Kaminoan scientist and passes AZI-3 who is similarly being escorted in the opposite direction. Fives says a farewell to the helpful little droid. AZI-3 asks if Fives is being reprogrammed, like AZI-3 will be. He has heard that Fives is scheduled to be mindwiped and placed on sanitation detail. This stirs Fives into action, and he bowls over the guards and makes a run for it, with AZI-3 in tow. Alarms blare throughout the corridors.

Fives runs back into the observation room, where he finds the original tumor in the sample box. This confirms his suspicions that Nala Se is up to something. Fives and AZI-3 rush to the hangar bay, where the desperate ARC trooper knocks unconscious a clone pilot and steals a Kaminoan flight pod. The spherical ship blasts off and speeds across the ocean as Shaak Ti and her clone security team arrive. She orders the ship tracked and Fives brought in alive.

Fives sets the pod on autopilot and bails from it, landing in the ocean with AZI-3. His plan is to have the pursuing clones follow the pod as a diversion while he returns to the city to investigate. AZI-3 reconfigures his chassis into a survival mode -- a speeder-bike like mode that Fives can ride back to Tipoca City.

Nala Se confers with a hologram of Darth Tyranus, and she informs the mysterious man that a renegade clone has stolen the inhibitor chip sample. Tyranus is deeply concerned regarding this aberrant behavior among the clones. Nala Se chalks Fives' rebelliousness to creative impulses inspired by working alongside Jedi Knights. She assures Tyranus that it does not mean that the contingency protocol 66 is in any way compromised. Tyranus orders her to find Fives immediately and recover the chip.

Fives and AZI-3 fly back to Tipoca City, entering the underside of the stilt-city via an irising maintenance portal. Inside, AZI-3 helps Fives procure a new set of armor by luring a clone trooper into a storeroom, where Fives knocks him unconscious.

Suitably disguised, Fives and AZI-3 next visit the genetic records hall to analyze the tumor sample. The large room has workstations that have access to data on the original DNA of every being the Kaminoans have ever cloned. By comparing the tumor with the original donor template, AZI-3 can quickly scan the archives to see if any anomaly like this had ever occurred before. An initial scan turns up negative: it does not match anything in the Jango Fett genotype, and furthermore it is a foreign implant.

Fives notices that the Kaminoans are beginning to exit. He and AZI-3 leave through an emergency access hatch just as Shaak Ti, Nala Se and their security team arrives. AZI-3 welds the access hatch shut behind him, allowing Fives and the droid to escape into the anti-flooding ductwork that weaves its way throughout Tipoca City.

AZI-3 theorizes the tumor is some sort of organic construct made of cells that was slipped into Tup at some point, but cannot conjecture as to why. Fives worries that he too carries such a chip, and wants AZI-3 to remove it if that is the case. AZI-3 cautions that such a procedure is risky; Tup died after his surgery, after all. But Fives is willing to take the risk and he trusts AZI-3. The two fugitives make their way to a sterile facility.

In an unoccupied surgical suite, AZI-3 sedates Fives and performs the operation. As Shaak Ti and Nala Se continue their search for Fives, he awakens from surgery. His head is shaven and he has a large bandage covering the surgical incision. AZI-3 was successful -- he found the organic chip within Fives' brain. Fives' sample is healthy and intact while the one extracted from Tup appears black and decomposing; the latter had clearly malfunctioned.

Fives and AZI-3 sneak into the training areas of the clone hatcheries, past young clones undergoing training. Though they try to blend in, their presence is reported as suspicious by several observant Kamino overseers. Nala Se receives the alert first, and attempts to act without drawing Shaak Ti's attention. Fives and AZI-3 arrive at the clone hatcheries, where embryos gestate in high-tech glass jars. Some detective work by AZI-3 reveals that all the clone embryos past stage three of development have an inhibitor chip implanted into their brains.

Nala Se enters the room and Fives holds her at gunpoint, demanding answers. Nala Se explains that the implants are structural inhibitor chips that are supposed to prevent clones from being overly aggressive. They were implanted at the order of Jedi Master Sifo-Dyas. Fives is shocked to discover this was done at the Jedi's behest.

Shaak Ti arrives, having followed Nala Se with a clone security detail. She orders Fives to drop his weapon. Fives shouts that he has evidence of a conspiracy -- that Tup's aberration was the result of a malfunctioning inhibitor chip. He demands that the chips be removed from the entire clone army. But Nala Se says there is no proof of the causality of his claims, and that the removal of the chips would be dangerous. Fives countered that he has had his removed.

Nala Se is shocked. With his inhibitor chip removed, Fives is now a risk that must be contained. Despite Nala Se's objections, Shaak Ti decides that Fives must go to Coruscant, and explain his story to the Supreme Chancellor.