A flaw in the plan! While in the middle of a heated battle, clone trooper Tup lost his senses and killed a Jedi general. Seeming to have no awareness of his actions, Tup's health began to deteriorate rapidly. Fearing the illness was linked to a Separatist plot, Anakin Skywalker has dispatched Captain Rex and ARC Trooper 5555 to escort Tup back to the cloning facilities on Kamino for an intensive evaluation....

The Republic medical frigate settles on the rain swept landing platform of the principal cloning facility in Tipoca City. The Kaminoan scientist Nala Se and a contingent of clone troopers stand at ready to receive Tup, who lies unconscious atop a hovergurney guided by Clone Captain Rex and ARC Trooper Fives. Nala Se directs Tup to a separate chamber, and the visiting clones are greeted by Jedi Master Shaak Ti.

Since Fives worked directly with Tup for the longest time, Shaak Ti wants him to undergo a medical evaluation, to see if there is any indication of contagion. Fives doesn't want to leave Tup's side, but Shaak Ti assures him that Tup is in good hands, what with Nala Se being the Chief Medical Scientist on Kamino and one of the primary engineers of the cloning program.

Shaak Ti tells Rex that General Skywalker has ordered him back to the frontline, so Rex departs, wishing Fives luck in looking out for Tup.

Fives and Tup are kept in adjacent observation rooms separated by a glass partition. Nala Se administers a stimshot to Tup, who begins violently convulsing as he undergoes a "hyper test." This is a normal reaction, but it worries Fives, who demands answers. Shaak Ti dims the partition between the rooms, cutting Fives off from seeing what the Kaminoans are doing to his friend.

The hyper test promptly begins delivering data. Tup shows no sign of infection. Indeed, clinically speaking, he is in perfect health. When Tup stops convulsing and focuses for a minute, his eyes lock onto Shaak Ti. He begins murmuring about following orders, and killing the Jedi. Shaak Ti is alarmed; perhaps the Separatists have found a way to brainwash Tup? The medical droids sedate Tup.

In the next observation room, Fives paces the room nervously. A bright-eyed medical analysis droid, AZI-3, assures him that Tup's procedure will be over quickly, as will Fives' examination. Sure enough, AZI-3 quickly extracts a blood sample from Fives and declares his life signs to be normal. But Fives cannot leave the observation room yet until they have pinpointed the exact cause of Tup's breakdown.

As Tup's examination continues, Shaak Ti and Nala Se disagree about what the underlying cause of his condition might be. Shaak Ti believes it to be psychological, while Nala Se thinks it to be a viral infection. A phase one and phase two medical scan has not produced answers, and AZI-3 suggests a phase five atomic scan. Nala Se counters that the only way to find a definitive answer is to terminate Tup and molecularly examine his cadaver.

Shaak Ti is appalled by this suggestion. She pulls rank on Nala Se, claiming that the care of the clones is the responsibility of the Jedi Order. Nala Se counters coldly that their genetic makeup is the property of Kamino. However, out of respect to her client, she will bring the matter up to her superior, Prime Minister Lama Su. Shaak Ti likewise will confer with the Jedi Council.

In Fives' observation room, AZI-3 updates the impatient clone with news that Tup's condition is deteriorating. Fives objects to AZI-3 referring to Tup by his clone number, and stresses to the confused little droid that clone troopers are more than numbers.

Nala Se enters Prime Minister Lama Su's office. She reveals to her superior that Tup's condition appears to be the result of clone protocol 66 prematurely activating. She advises terminating the clone to allow for a detailed autopsy to discover why the implanted inhibitor chip malfunctioned. Lama Su is alarmed. He motions Nala Se to a more private chamber and makes holographic contact with Lord Tyranus.

Tyranus agrees with Nala Se's prognosis, and orders the Kaminoans to terminate Tup, however the inhibitor chip is to be sent to him immediately for analysis. Tyranus explains that the inhibitor chip must be kept secret from the Jedi -- it was devised as a means of countering rogue Jedi. The only other person to know of this genetic modification is the late Master Sifo-Dyas, and this secret has gone to the grave with him.

Shaak Ti holographically appears before the assembled Jedi Council on Coruscant. She stresses her belief that Tup has been brainwashed, and should not be dissected. She notes that Skywalker's battlefield reports have Tup listed as missing for five days during the Ringo Vinda campaign -- a point where he might have possibly been compromised.

Ti explains that the Kaminoans worry that further brain scans would damage the neural tissue, whereas an immediate termination and dissection would keep this tissue intact. Obi-Wan is off put by such talk of Tup as a specimen. He recommends to Shaak Ti that Tup be brought to the Jedi Temple for examination. Yoda concurs, suggesting that the Jedi Council could examine him through the Force.

Back in Fives' observation room, Fives believes Tup would be willing to risk his life to find a cure. He is determined to get the atomic brain scan. Fives fast-talks his way past AZI-3's programmed protocols to bend rules to save Tup's life at all costs. Fives and AZI-3 sneak their way into Tup's observation room where AZI-3 gets to work.

Tup is placed in a medical scanner. A close look reveals an anomalous growth in Tup's brain -- a tumor. AZI-3 must take a biopsy for a closer look.

Nala Se hears commotion in the observation room and enters. Fives hides behind the equipment, while AZI-3 explains to an impatient and incensed Nala Se why he performed an unauthorized scan. The little droid reveals his discovery of the tumor, which blocks neuro-impulses from within the brain. Nala See corrects the droid -- he did not find a tumor. The clone, she persists, has a viral infection. She plans to continue with the termination.

Fives leaves the room and cannot believe that Tup will be so coldly disposed, especially in the face of their newfound evidence. He tells AZI-3 to continue with the biopsy, and they will deliver their results to Shaak Ti. He has AZI-3 hack into the security mainframe and trigger an intruder alert, which interrupts Nala Se's procedure.

As per protocol, Nala Se and Lama Su leave the observation room to head to a safe room for lockdown. With the chaos of the alarm as cover, AZI-3 breaks into Tup's observation room and extracts the tumor with some quick, skillful surgery.

Shaak Ti learns that the intruder alert is a false report originating from the medical bay. She surmises that Fives must somehow be behind this, and rushes to Tup's observation room. She and Nala Se arrive just as Tup awakens from surgery. Tup groggily says that he is free now, that his mission has completed. He declares his nightmare is over before succumbing to death in Fives' arms. Clone guards surround Fives, shackling him and placing him under arrest.

Shaak Ti and Nala Se communicate with Supreme Chancellor Palpatine, informing him that the quarantined clone has died. Shaak Ti recommends the clone's body be sent to the Jedi Temple, but Palpatine suggests instead he be brought to the state of art Grand Republic Medical Facility. Nala Se concurs, and Shaak Ti, with some hesitance, also agrees.