Following the capture of Maul and a victory in the Siege of Mandalore, a calm washes over the planet's city streets. Bo-Katan greets Ahsoka, and they discuss the future of Mandalore, but the Togruta is soon pulled away to a conference with the Jedi.

In a secret meeting, Mace Windu reveals that he senses a plot to destroy the Jedi. "The dark side of the Force surrounds the Chancellor," he says. As Ahsoka joins, she informs the Council that she has captured Maul; she and Rex will soon deliver him.

Ahsoka asks for Anakin, but Windu has just sent the Jedi to tell Palpatine that they've located General Grievous. Tano expresses some optimism that destroying Grievous could mean the end of the war. "That depends on the Chancellor," Windu replies, though he will discuss matters no further with Ahsoka, who is not a Jedi.

The Mandalorians bring Maul, secured in mobile cell designed to hold Force-wielders, to the Republic forces. Bo-Katan and Ahsoka bid their goodbyes, clearly having earned each other's respect.

Back on the Republic cruiser, clones transport Maul to a holding cell. Rex and Ahsoka go to the bridge, but Tano's thoughts are elsewhere. She says that Jedi are meant to be peacekeepers, not soldiers -- but war is all she's ever known as a Jedi. Rex says that the clones have mixed feelings about the war; without it, they would not exist. Tano replies warmly, stating that the Republic could not have had better soldiers, nor she a better friend. The two salute each other, before Rex departs for the latest briefing.

But from Ahsoka's position on the bridge and Maul's from his cell, both sense a disturbance in the Force. Something has happened to Anakin. Ahsoka hurries to find Rex, who is at the end of his briefing, which Palpatine closes with a new command: "Execute Order 66."

Ahsoka begins to tell Rex of her fears that something terrible has happened, but he only looks forward, gripping his helmet intensely before dropping it. Then, two clones behind Ahsoka raise their weapons. "No!" shouts Rex. "I'll do it." Tano, confused, tries to talk sense into her friend, but to no avail. Rex points his blasters at Ahsoka, muttering something about Fives, before firing!

Tano leaps toward her friend, tackling him as the other clones open fire. She deflects their shots back, killing them, then flees as more troopers enter the bridge. As the dust settles, Rex commands his troops to go execute Maul, then reiterates Palpatine's directive: all Jedi are to be executed for treason, and any clone that does not comply will also be killed. He then dispatches the soldiers to hunt Ahsoka down.

The clones arrive at Maul's cell, and the Zabrak's eyes race with fear. They open his coffin-like chamber, ready to destroy him -- but Ahsoka Tano soon appears, knocking the soldiers unconscious. "Don't make me regret this," she says, freeing Maul.

Maul assures her this is not his doing, but says he has felt "death." When Tano says that her clones turned against her, Maul seems almost impressed. "Brilliant!" he says of his master's plot. "He turned the Jedi's own army against them." But Ahsoka will not team up with Maul; she only wants him to cause chaos and create a diversion.

Tano moves through the ship, and finally finds a group of droids: R7-A7, RG-G1, and CH-33P. They agree to help her, and she asks one astromech to bring up every file on Fives. She discovers a recording of a Kaminoan cloner, discussing an inhibitor chip malfunction, and then opens Rex's confidential grievance report -- using Anakin's password. In the report, Rex says there's a possibility that the inhibitor chips "have a purpose that we don't fully understand."

Meanwhile, Maul makes his way through the cruiser, obliterating all in his path. He holds onto a comlink from a fallen soldier, allowing him to monitor Republic chatter.

As Rex continues to search for Maul and Tano, one of Ahsoka's droids suddenly blocks his path. Then, the other astromechs seal the blast doors around him. R7-A7 plays a transmission from Ahsoka, who says that she's seen Rex's report on Fives -- the clones were programmed to turn on the Jedi. "I can help you," she says to Rex. When Tano reveals herself, standing right behind Rex, a droid stuns the commander and they carry him to the medical bay.

The droids scan Rex looking for the chip, but time is running out as the clones work on opening the door. Unable to detect a foreign device, Ahsoka gently touches Rex's face and repeats the words, "I am one with the Force, and the Force is with me." Soon, Rex chants in unison, and the chip appears on-screen. "R7, get him under and remove that thing," Ahsoka commands, unsure if he'll survive the procedure.

Tano readies her lightsabers as the clones break through. She deflects their attacks with amazing skill and precision, but there are too many, and the blasts drive her back. Suddenly, however, the clones fall as cover shots are fired from behind her, and R7 locks the door.

Rex, waking from the surgery, saved his friend. He apologizes for what he had tried to do, and relays the horror of Order 66. "Ahsoka, it's all of us," he says. "The entire Grand Army of the Republic has been ordered to hunt down and destroy the Jedi Knights."