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.