With the Republic gaining the upper hand in the Clone War, Jedi Master Depa Billaba leads her troops in battle on Kaller. But they need help. Her Padawan, Caleb Dume, promises that reinforcements are on the way. "You've gotta see these clones," he says. "They're different."

Suddenly, a team of clones attacks the droids of the Separatist Army! With uncanny precision, they methodically destroy the entire battalion.

Following the battle, Caleb introduces the unique squad to his master: Wrecker, Hunter, Echo, Tech, and Crosshair, also known as Clone Force 99, or more informally, the Bad Batch. Her actual reinforcements have been rerouted to Coruscant, they inform her; meanwhile, Tech relays a comm saying that Obi-Wan Kenobi has engaged General Grievous. The war may soon be over.

But something is wrong. Depa's clone commander receives a transmission from the Supreme Chancellor: "Execute Order 66." Instantly, her clones open fire; with her last act, Depa commands Caleb to run.

The Padawan flees from Clone Force 99, though the Order 66 command seems to mean nothing to the Bad Batch. Hunter and Crosshair go to find him.

Soon, Tech contacts Hunter and explains that the "regs," or regular clones, have been ordered to execute all Jedi for treason. Hunter can't believe it. But in that moment, Crosshair spots and fires at Caleb, surprising Hunter.

Caleb ignites his saber and charges. Hunter tries to diffuse the situation, throwing his weapon away. "I'm on your side," he says, but the frightened Padawan runs once more.

Hunter corners Dume at a cliff's edge, imploring that he can help him. But when he hears the chatter of regular clones, the boy turns and leaps across the ravine, escaping into the woods. Hunter, protecting the boy, tells Crosshair that he didn't survive the jump.

The Bad Batch return to Kamino, homeworld of the clones. Curiously, they're asked to provide a clearance code to land.

They soon learn that General Grievous has been defeated and the war is over. But Hunter is alarmed at the presence of Coruscant shock troopers, and suspicions continue to rise when a body moved by clones drops a lightsaber to the floor. The Bad Batch decide to retreat to their barracks.

In their quarters, Crosshair challenges Hunter, and says he's been lying about the Padawan. "An order is an order," he says, claiming they should've killed the boy. Tech asserts that the regs were engineered to follow orders, which is why they turned on the Jedi so easily; the Bad Batch, with their mutations, contain no such programming. Echo's experience on Skako Minor most likely removed any earlier genetic obedience to the Chancellor.

The Supreme Chancellor holds a special session, detailing the betrayal of the Jedi and the reorganization of the Republic into the Empire. As the clones cheer around them, the Bad Batch stand stoically. Mysteriously, a child, watching from above, sees Hunter but then seems to disappear.

The child stops the Bad Batch in a corridor. She introduces herself as Omega, and seems to know a lot about the Bad Batch. One of the Kaminoans, Nala Se, claims that Omega is her medical assistant before calling her away.

Admiral Tarkin comes to Kamino. He informs Lama Su, the Kaminoan prime minister, that Emperor Palpatine is terminating their deal, and will shift to a more affordable conscription military.

The Bad Batch discuss recent events in the cafeteria, and are soon joined by Omega. "I like you," she says. "You don't fit in around here, either." But as a passing clone taunts the Bad Batch, Omega stands up for her new friends, throwing her food tray right in the clone's face.

Though Hunter once again diffuses the situation, matters soon escalate when Wrecker tosses a stack of trays at the offending clone and his friends. With that...

...chaos erupts.

Later, Echo wakes up in lab but panics upon seeing a medical droid. Omega, however, calms him down, and soon the Kaminoan prime minister summons Clone Force 99.

Omega wants to go with them, but Hunter says no. As the group heads toward the meeting, shock troopers interrupt and tell them to go to the training facility. They are to be tested by Tarkin.

The training sequence begins, and the Bad Batch make easy work of their droid combatants. Nonplussed, Tarkin commands that the droids switch to live fire for a real test. He does not inform the Bad Batch of the alteration.

As the training exercise continues, Wrecker charges into battle...only this time, he suffers a blaster shot and falls backward! The hulking clone crawls his way back to his squad, and they hide behind cover. Armed only with training blasters, they'll have to improvise.

On Hunter's orders to try an old tactic, Wrecker wrestles a droid to the ground. Tech reprograms it to fight on their side, and the Bad Batch soon win the battle.

Later, Tarkin asks the Kaminoans about Clone Force 99, impressed by their skill but worried about their independent streak. The prime minister assures that their reluctance to follow orders has never hindered their ability to complete a mission. Upon hearing this, Tarkin raises the question: Did they follow Order 66? A counter report filed by a member of the Bad Batch says a Padawan escaped their grasp. Indeed, he says he will soon test their loyalty.

As the Bad Batch debate recent events in their quarters, Tarkin arrives. He has a mission for the group: Eliminate the insurgents on Onderon.

Hunter walks to their ship and Omega catches up to him, worried. "I don't trust him," she says of Tarkin. Omega is scared and says they need to leave Kamino, but Hunter won't let her come with them.

The Bad Batch arrive on Onderon in the dead of night. But instead of Separtist droids, they find only people. Crosshair is eager to pull the trigger but Hunter won't give the order to fire; in their delay, an armed militia quickly surrounds the clones.

The rebels take the Bad Batch to their camp, and are soon joined by the leader of the supposed insurgency: Saw Gerrera. Tech knows who he is -- Gerrera was trained by clone captain Rex and Jedi general Anakin Skywalker to fight for the Republic. "Why don't you take a look at the insurgents you were sent to destroy?" Gerrera says, motioning toward the civilians he protects, including children.

Saw does not believe the Emperor's story. He says that with the Jedi decimated and the clone army under his command, Palpatine will control the galaxy unopposed. They have to stop him, or the Clone War will have been for nothing. "The clones once helped us free Onderon, so we'll give them a choice," Saw says, returning Hunter's weapon. Meanwhile, a probe droid watches from the trees...

As they return to their ship, tensions rise. Crosshair wants to complete the mission, and says Hunter isn't fit to lead if he cannot follow orders. Suddenly, Hunter opens fire -- blasting the probe droid. He says Omega warned him about the mission and Tarkin.

Back at the ship, Tech confirms that Omega is the same as them -- a mutated clone. Hunter decides to return to Kamino for the girl, overruling Crosshair's objections.

Meanwhile, Omega looks around the Bad Batch's quarters on Kamino. But shock troopers soon come and apprehend her.

When the Bad Batch arrive at Kamino, they're quickly surrounded upon entering the hangar. "The Empire does not tolerate failure, sergeant," Tarkin says, claiming treason.

The Bad Batch are thrown in the brig, where they also find Omega. "You came back for me?" she says excitedly. Still, Crosshair continues to needle Hunter, growing more and more angry. "Good soldiers follow orders!" he bellows. Hunter doesn't take the bait.

Crosshair sits alone, and Omega joins him. "I know what you're going to do, but please don't," she says. Still, Omega claims that it will not be his fault.

Clones come and take Crosshair. The sharpshooter is loaded into a scanner, where Nala Se and Tarkin examine his cranial activity. Though not as functional as those in normal clones, Crosshair's inhibitor chip appears to be working. Tarkin orders the programming to be intensified.

Back in the cell, Tech has an idea. This facility is not a prison, he realizes, and it wasn't built for someone like Wrecker. If the large clone hits the wall in just the right spot, they'll be free. After a couple of wallops, a small dent appears...which Tech then peels back. It's just big enough for Omega to crawl through! Now she can make her way into the control room and deactivate the ray shield.

The guards realize that Omega, now in the vents, is missing. As they question the Bad Batch, Omega watches from above and then slams the grate beneath her -- bringing it and herself down upon the shock troopers. She runs to the controls and hits the switch, freeing her friends.

The Bad Batch go their ship to gear up for their search for Crosshair, with Omega in tow. But Crosshair, leading a squad of clones, finds them first. "You never could see the bigger picture. Now surrender," he says to Hunter. They stare each other down...until, finally, Crosshair shoots at his former friend, and a firefight erupts.

Both sides exchange fire in the smoky, darkened hangar. After Wrecker clears out most of the troopers, Crosshair takes his shot, blasting his old squadmate. As Tech readies the ship, Crosshair orders the bay door closed...which Nala Se secretly overrides from the control room.

Finally, Crosshair has Hunter in his sights. But just as he's about to squeeze the trigger, Omega blasts the rifle from his hands. The Bad Batch and Omega make their escape.

Nala Se reports to the prime minister that Clone Force 99 have escaped with Omega. The prime minister orders she say nothing.

On board their shuttle, Echo gives Wrecker some meds...and Omega returns his tooka doll. "You found my Lula!" Wrecker says.

In the cockpit, the Bad Batch decide what they'll do next. Omega asks if they have any friends that can help. Hunter thinks of one and commands that they plot a course for J-19. "Strap in kid," he says to Omega as they prepare to jump to lightspeed. "You're not gonna want to miss this view."