Season two
Episode one
Clone Force 99 are back and after concluding another perilous mission they're offered a new job that could set them up for life. Echo, Tech and Wrecker have a different opinion from Hunter in regards to if they should take on this heist and the implications that it could have on Omega.

Episode two
The heist isn't going according to plan due to the location being owned by Count Dooku and heavily guarded by storm troopers. A local provides the group with help. Within the Empire information about Clone Force 99 still being alive after rumours of their death cause friction and a loose end needs to be tied up.

Episode three
Crosshair is given a mission to travel to Desix and he's assigned to work with Commander Cody. An uprising is happening and it is their job to enforce the rule of the empire.

Episode four
We spend most of our time this episode with Omega, Tech and Wrecker as they have to go to a pod racing event. But the people they're supporting are up against some rivals that are willing to do whatever it takes to win.

Episode five
The batch head off on a treasure hunt with Cid's friend Phee. But everything doesn't go to plan when the loot they were seeking to pillage has an adverse effect on their surroundings.

Episode six
As the Batch are in the process of doing a deal with some droids, Omega hears a cry for help. The captive is rescued by the team and a path is made to ensure they are placed somewhere safe within the galaxy. But the Empire is everywhere, so the Batch do what they do best and dispose of anyone that gets in their way.

Episode seven
A clone is assassinated by a sniper causing his fellow clone to go on the run. On Corusant a political conspiracy is unfolding in regards to what happened on Kamino.

Episode eight
The Batch enter the story with the mission of retrieving some essential data. The conspiracy is revealed in the Senate and a new plan is implemented.

Episode nine
After Echo joins Rex on his quest, the Batch have to do another job for Cid. But everything keeps going wrong. Omega is struggling to deal with recent events and opens up to Tech about it. He states that change is inevitable and also an opportunity for growth.

Episode ten
The batch are on the trail of who took their ship. But the reasons as to why that person took the ship and the environment they inhabit are expanded upon.

Episode eleven
Cid continues to hold the batch to ransom and sends them off onto another mission. But this doesn't go to plan at all and not only endangers them but also innocent civilians too. This disaster also catches the attention of the Empire, who gain something from this and are looking to gain even more.

Episode twelve
Crosshair is assigned by the Empire to carry out a mission to retrieve something important. He is told he needs to team up with another clone on this quest. It doesn't go to plan when they discover what they are tasked with obtaining and the reasons why.