When Order 66 prompts the Clone Troopers to turn on the Jedi and support the new Galactic Empire, a unit of "defective" clones must decide which side they are on – and how they can help a mysterious girl who is working with the Kaminoans.

After deserting the Empire, Clone Force 99 seeks refuge with a fellow deserter on the planet Saleucami, where Hunter realizes that he can't give Omega what she needs.

The Bad Batch and Echo must make repairs after crash-landing on a desolate moon. Elsewhere Tarkin puts the Empire's new army of recruits to the test, while Crosshair seeks to prove his worth.

After the team lands in order to disable their ship's transponder, a local sells them out to a bounty hunter – who tries to capture Omega.

To gain some credits and the help of a former Jedi informant the team agrees to rescue a child from a group of slavers ... unaware of what they are actually getting themselves into.

Cid tasks the team to break into an Separatist facility on Corellia to steal a decommissioned tactical droid.

The Bad Batch is surprised by the apperance of Captain Rex, a clone commander who insists that they must remove the inhibitor chips inside their brains -- leading them to a derelict Jedi cruiser.

The Bad Batch's attempts to scavenge weapons and intel from a downed Jedi cruiser are cut short by the arrival of an Imperial retrieval squad, led by Crosshair, who is bent on taking out his former teammates.

Cad Bane attempts to deliver Omega to the cloners, only to run afoul of a fellow bounty hunter looking for a big score.

The Bad Batch responds to a distress call from the planet Raxus, where the Empire has occupied the planet and imprisoned the Separatist Senator who stood up to them.

As the planet Ryloth is occupied by "friendly" imperial forces, General Cham Sydulla and his wife struggle with their planet's new alliance – while their young daughter falls in with a growing resistance movement.

After her parents are taken into custody Young Hera Syndulla transmits a distress call to Omega, bringing Clone Force 99 back to Ryloth in a risk mission to free them – and potentially spark a new resistance movement.

After the squad discovers that Cid's place has been usurped by a crime boss, Cid recruits them to steal from him in order to compromise his position with the dangerous Pyke Syndicate.

An old friend tasks the team with rescuing a clone from an Imperial facility on Daro, where they find a new kind of army in the employ of the Empire.

The team is drawn back to Kamino in the hopes of rescuing one of their own, knowing that Crosshair is luring them into a trap.

After their reunion with Crosshair the squad fights for survival by making their way through the ruins of Kamino, which the Empire has laid waste.