The Jedi Temple is in disarray after a vicious terrorist attack. Anakin Skywalker and Ahsoka Tano set out to find the truth of who was really behind this horrendous catastrophe. Their investigation led them to discover the true saboteur, Letta Turmond. Now the Jedi attempt to return the Temple to normalcy. But first Master Yoda must give a eulogy to the fallen Jedi warriors.

Within a chapel of the Jedi Temple, the Masters of the Order are joined by Republic Senate and military dignitaries to honor the six Jedi Knights killed in the hangar blast. After Yoda delivers a stirring eulogy, the Jedi and officials file out.

Ahsoka hears from Admiral Tarkin that Letta Turmond has been moved from custody within the Temple to a military facility. Tarkin firmly explains to an incredulous Ahsoka that since clones were killed in the attack, and since the accused is not a Jedi, it is indeed a military matter, not a Jedi affair. Ahsoka is emotional -- she does not want Letta to avoid punishment. Anakin warns her to temper her emotions.

As Anakin and Tarkin continue along, Ahsoka parts ways and walks with her friend Barriss Offee. Barriss wonders whether or not Ahsoka is wrong to feel so emotional. Ahsoka puts up a strong front, but their conversation is interrupted as she is called to the war room with word of a Separatist attack on a distant system.

Ahsoka attends the strategy briefing, but is summoned by Admiral Tarkin. Letta Turmond would like to speak with her. Ahsoka is surprised by this, but obliges, traveling to the Republic military base. Clone Commander Fox disarms Ahsoka and lets her into Letta's cell.

A nervous Letta reveals that it was a Jedi behind the bombing -- a Jedi had sided with her political beliefs that the Order had compromised itself by supporting the war. This Jedi accomplice supplied Letta with the nano-droids and taught her how to turn them into a weapon. Letta believes she has been set up to take the fall for this conspiracy.

Ahsoka is skeptical. She demands to know the identity of this Jedi, but Letta will only reveal it if she gets protection. Letta was told that if she was ever in trouble, Ahsoka would be the Jedi to help her. As Letta begins to reveal the Jedi's identity, her voice halts mid-speech. She is choked by an unseen Force. Ahsoka reaches for her, attempting to save Letta's life.

The security clone troopers see only Ahsoka reaching for Letta as Turmond chokes to death. They rush the cell, but Letta is already dead. Though Fox feels Ahsoka was justified in killing a traitor to the Republic, he has no choice but to arrest Ahsoka.

Ahsoka is imprisoned at the Imperial facility. She is visited by Tarkin, who reveals to her that her encounter was recorded with security cameras. Strangely, the images were recorded without sound, which makes Ahsoka's encounter with Letta look very damning. Anakin, angered by the situation, comes to check on her, but Clone Commander Fox will not let him in, as per Admiral Tarkin's orders.

Ahsoka awakens in her cell after some fitful sleeping to find a key card on the floor outside her cell. Assuming that somehow Anakin is helping her, Ahsoka lifts the card with the Force and uses it to unlock her cell.

Sneaking down the hall, she is shocked to discover several clone troopers knocked unconscious. Lying on the floor next to the incapacitated clones are her lightsabers and comlink. She scoops them up just as Clone Commander Fox arrives and jumps to a terrible conclusion. Fox sounds the alarm and puts the facility on lockdown.

Ahsoka runs from the clones, flipping through closing blast doors and turning blind corners. Reaching an intersection, she is dismayed to find three dead clone troopers, killed by a lightsaber. Fox opens fire, and alerts the security team to shoot-to-kill. Captain Rex and Anakin arrive, and Skywalker immediately countermands Fox. Rex cannot believe Ahsoka would have killed clones.

Anakin calls out to Ahsoka for her to stop running. He believes in her innocence. Ahsoka realizes someone is setting her up, and refuses to surrender. Skywalker takes command of the search for Ahsoka. Rex puts out an APB for the fugitive Padawan.

Ahsoka sneaks her way outside the base. She climbs along the base walls, avoiding clone trooper patrols. Captain Fox spots her making her way to her speeder. A heavy weapons emplacement destroys her escape speeder, leaving her stranded on the base. She dashes towards an adjacent industrial pipeline. Anakin catches up with Fox, and orders weapons set to stun. He wants her taken alive.

Stun beams wash against the gantries and pipes that crowd the industrial space. Ahsoka dodges and deflects the beams as she frantically tries to outrun the clones.

From a gunship, Oddball shines a spotlight on Ahsoka as she runs across the central viaduct. As rain starts to fall, a near-miss from a clone causes Ahsoka to drop one of her lightsabers.

She is soon surrounded by clone troopers, and cuts her way into one of the massive pipes.

Anakin and a squad of clone troopers follow. Sensing Ahsoka in the Force, Anakin breaks off from the rest of the clones and finds Ahsoka standing at a dead end -- a massive drop from the end of a water pipe into a huge portal that opens into the underworld of Coruscant.

Anakin implores Ahsoka to surrender so she can prove her innocence. Ahsoka is desperate. Though she trusts Anakin, she realizes something much bigger is working against her. With a farewell to her Master, she leaps from the pipe into the depths below.