Escape from the Republic military base

Following the bombing at the Jedi Temple, which resulted in the deaths of several Jedi, clone troopers, and Temple employees, Jedi Knight Anakin Skywalker and his Padawan, Ahsoka Tano, discovered that Letta Turmond, the spouse of a Temple worker named Jackar Bowmani, had administered nano-droids to her husband. These droids subsequently detonated while Bowmani was working inside the Temple. The Jedi arrested Turmond, who was later transferred to the military's custody upon the request of Supreme Chancellor Sheev Palpatine. While confined at the Republic military base, Turmond requested a meeting with Padawan Tano.

Suspecting Turmond's intentions, Padawan Tano decided to personally question the inmate to gain insight into the motivations behind the murder of her fellow Jedi. Turmond disclosed that she had been contacted by another Jedi, who had become disillusioned with the Jedi Order. This Jedi had requested her to provide the nano-droids to Bowmani. However, before Turmond could identify that Jedi as Barriss Offee, Offee used the Force to choke her, having concealed herself, thereby implicating Tano in Turmond's murder. Clone Commander Fox of the Coruscant Guard, witnessing Turmond being choked on the monitor screen, stormed in with two other troopers and arrested a bewildered Tano on suspicion of murder. After reviewing the video footage, which lacked audio but appeared to depict Tano choking Turmond, Admiral Wilhuff Tarkin deemed Tano guilty, considering her dissatisfaction with Turmond being placed under military authority. Tarkin then prohibited visitors, especially Skywalker, who was compelled to leave after demanding access.

Following a short period in a holding cell, Tano noticed a security access card lying on the floor, just beyond the force field blocking the door. Presuming it had been left by her mentor, she used the Force to levitate the card and used it to break free from her cell. Moving through the corridors, Tano discovered lightsabers and a comlink amidst several unconscious troopers. As she was answering her ringing comlink, Commander Fox entered the security observation room and, upon seeing Tano among the incapacitated clones, immediately concluded she was responsible and activated the alarm. Instead of confronting Fox, Tano fled, attempting to escape the facility. After avoiding several clone patrols, Tano encountered three deceased clones, killed with a lightsaber. A pursuit throughout the facility ensued, with Fox issuing orders to shoot to kill, until Anakin Skywalker and Clone Captain Rex arrived and intervened, at which point the troops were instructed to only fire stun blasts and capture Tano alive.

All clone shock troopers were alerted throughout the base, and the search extended to the landing area outside the base and past the memorial. It was there that the shock troopers spotted Tano and pursued her with an increasing number of troopers and LAAT/i vehicles. During the chase, while deflecting stun bolts, one clone fired a rocket launcher, causing her to fall. As she dropped her lightsabers, Tano grabbed one before continuing to run. Eventually, Tano was cornered but managed to escape again by cutting into a nearby piping system. She evaded the troopers before reaching the end of the pipe, which led to a sinkhole towards the Coruscant Underworld. Skywalker located her and implored her to return, arguing that escaping would only worsen the situation. However, Tano refused to be punished for crimes she had not committed and asked him to trust her as she trusted him while she was searching for proof of her innocence. As Rex and Fox caught up to Skywalker, Tano jumped onto a transport descending into the underworld.

Following the escape, the Jedi High Council commanded Tano's arrest, assigning Skywalker and Jedi Master Plo Koon to the task. Ultimately, Tano was recaptured after Barriss Offee, in disguise, lured her into a trap, and she was returned to the Jedi Temple.

As the Council deliberated on Tano's fate, Tarkin requested—on behalf of the Galactic Senate—that Tano be removed from the Jedi Order and returned to military custody for a military tribunal. Although not in complete agreement, the Council complied with the Senate's request, expelling Tano and returning her to the Republic military prison. Tano was subsequently put on trial before members of the Senate, with Tarkin serving as the prosecutor and Senator Padmé Amidala acting as the defense. However, before the jury could reach a verdict, Skywalker, having conducted his own investigation, entered the room with Offee. She finally confessed to her crimes, thus exonerating Tano and resulting in Offee's imprisonment in her place. Nevertheless, Tano declined to rejoin the Jedi Order when offered readmission, as her faith in the Order had been compromised due to their disbelief in her innocence.