| No.overall | No. inseason | Title | Directed by | Written by | Original release date |
| 1 | 1 | "Aftermath" | Steward Lee, Saul Ruiz & Nathaniel Villanueva | Jennifer Corbett & Dave Filoni | May 4, 2021 (2021-05-04) |
| Clone Force 99, also known as "The Bad Batch", includes defective clone troopers Hunter, Tech, Crosshair, and Wrecker plus cyborg clone Echo. During the Clone Wars, the Bad Batch assists Jedi Master Depa Billaba and her Padawan learner Caleb Dume on Kaller. Order 66 is issued, triggering programming in the regular clones that makes them kill Billaba. The Bad Batch receives the order too, but only Crosshair feels compelled to obey it, and Hunter lets Dume escape. Returning to the clone facilities on Kamino, the Bad Batch learns that the war is over and an Empire has replaced the Galactic Republic. They meet a young girl, Omega, who is another defective clone. Admiral Tarkin arrives to evaluate the clones and sends the Bad Batch to eliminate insurgents on Onderon. When they discover that these "insurgents" are refugees under Saw Gerrera who refuse to submit to the new Empire, the Bad Batch abandons the mission and returns for Omega. They are arrested for treason, and Tarkin enhances Crosshair's programming, turning him against his squad. The rest of the Bad Batch flee with Omega. |
| 2 | 2 | "Cut and Run" | Steward Lee | Gursimran Sandhu | May 7, 2021 (2021-05-07) |
| The Bad Batch and Omega seek refuge on Saleucami with clone deserter Cut Lawquane, who tells them about the inhibitor chips that programmed the regular clones and Crosshair to be loyal to the Empire after Order 66. With increased military presence from the Empire, Cut plans to escape with his family, but they need newly introduced chain codes to book public transport. Cut would be arrested if he tried to obtain chain codes, so Tech and Echo steal some, and Omega helps deliver them to Cut and his family in time for them to board the transport. Hunter wants Omega to go with Cut so she can have a family, but she decides to stay with the Bad Batch. |
| 3 | 3 | "Replacements" | Nathaniel Villanueva | Matt Michnovetz | May 14, 2021 (2021-05-14) |
| The Bad Batch's ship, the Marauder, is damaged on Saleucami. They are stranded on a moon and an Ordo Moon Dragon steals the part they need to repair the ship. Hunter and Omega set out to retrieve it. When Hunter is incapacitated, Omega continues alone and retrieves the part without a fight. On Kamino, Tarkin and Vice Admiral Rampart put Crosshair in command of a new unit of conscripted soldiers. They are sent to Onderon to wipe out Gerrera's camp, but Gerrera is already gone. Crosshair kills a disloyal recruit, but the rest comply and are otherwise successful. Tarkin sees potential for conscripted soldiers, concerning Kaminoan prime minister Lama Su. |
| 4 | 4 | "Cornered" | Saul Ruiz | Christian Taylor | May 21, 2021 (2021-05-21) |
| On their way to a proposed hiding-place on Idaflor, the Bad Batch is forced to stop on the nearest planet, Pantora, so they can gather supplies and Tech can modify their ship's signature since it now appears on the Empire's wanted list. A landing bay attendant on Pantora identifies the Bad Batch and informs Fennec Shand, a mercenary who has been hired to retrieve Omega. Hunter, Echo, and Omega search for supplies while Tech and Wrecker work on the ship. Omega is approached by Shand, which leads to Hunter chasing Shand through the city. Hunter and Omega lose Shand, and after the modifications are completed the Bad Batch departs from Pantora. |
| 5 | 5 | "Rampage" | Steward Lee | Tamara Becher-Wilkinson | May 28, 2021 (2021-05-28) |
| Hoping to discover who hired Shand, the Bad Batch goes to Ord Mantell where Echo knows of an informant named Cid. She offers to find out about Shand in exchange for their help: slavers have kidnapped a child named Muchi, and Cid will receive a reward from Jabba the Hutt if the Bad Batch helps her rescue the child. The Bad Batch finds and fights off the slavers, rescuing Muchi, who is a young rancor. Taking her to Cid, Muchi is then given to Jabba's right-hand man Bib Fortuna in exchange for the reward. Cid gives some of the reward to Hunter but is unable to learn who hired Shand. She offers to give the Bad Batch more mercenary work in the future. |
| 6 | 6 | "Decommissioned" | Nathaniel Villanueva | Amanda Rose Muñoz | June 4, 2021 (2021-06-04) |
| Cid hires the Bad Batch to retrieve a Separatist tactical droid with battle intel before it is destroyed at a Corellian decommissioning site. They run into smuggler sisters Trace and Rafa Martez, who are also after the droid. Wrecker's inhibitor chip begins to activate after he accidentally hits his head. Tech copies the tactical droid's data before it is destroyed when he and the sisters program it to turn on the police droids that are guarding the facility, allowing them to escape. The sisters explain that they were retrieving the droid for a client who is fighting the Empire, and Hunter decides to give them the data. Later, the sisters tell their client how to find the Bad Batch. |
| 7 | 7 | "Battle Scars" | Saul Ruiz | Jennifer Corbett | June 11, 2021 (2021-06-11) |
| After they fail to retrieve the tactical droid's data, Cid tells the Bad Batch that they will need to do a big job to pay off their debt to her. They are interrupted by the Martez sisters' client, former clone captain Rex, who is alarmed to learn that the Bad Batch have yet to remove their inhibitor chips as he has. They go to Bracca, a starship graveyard planet controlled by the Scrapper Guild, and sneak onto an old Jedi cruiser to use its medical bay. Wrecker's chip forces him to attack his squad mates, but he is subdued and the chip is removed. Rex takes his leave once the extractions are completed; as they say goodbye, Hunter is seen by members of the Scrapper Guild. |
| 8 | 8 | "Reunion" | Steward Lee | Christian Taylor | June 18, 2021 (2021-06-18) |
| The Scrapper Guild informs the Empire of the Bad Batch's location, and Crosshair is sent to kill them. Concerned that Omega will not be returned safely, Lama Su hires a second bounty hunter to retrieve the girl. The Bad Batch attempts to reach the Marauder through the Jedi cruiser's ion engine. Crosshair pins them inside and has the engine turned on, but they use explosives salvaged from the cruiser's armory to escape and Crosshair is injured by the engine's ignition. Hunter and Omega are confronted by bounty hunter Cad Bane, who shoots Hunter and kidnaps Omega. The rest of the squad catch up, carry the injured Hunter to the Marauder, and escape. |
| 9 | 9 | "Bounty Lost" | Brad Rau & Nathaniel Villanueva | Matt Michnovetz | June 25, 2021 (2021-06-25) |
| While chasing after Bane, the Bad Batch learns from Tech that Omega is an unmodified clone of Jango Fett and so is the only available source of fresh cloning material for the Kaminoans. En route to an old Kaminoan cloning facility on Bora Vio for her delivery, Omega tricks Bane's droid aide Todo into releasing her and is able to signal the Bad Batch. Lama Su sends Taun We to retrieve Omega and orders Nala Se to eliminate the girl after extracting genetic samples from her. Nala Se cares for Omega and wants to keep her safe, so she sends Shand to rescue her. Shand kills Taun We and duels Bane, allowing Omega to escape and be retrieved by the Bad Batch. |
| 10 | 10 | "Common Ground" | Saul Ruiz | Gursimran Sandhu | July 2, 2021 (2021-07-02) |
| On Raxus, which was the seat of the Separatist government during the Clone Wars, the Empire institutes new curfew laws with the support of local senator Avi Singh. However, Singh speaks out against the Empire while addressing the public and is arrested. His protocol droid GS-8 hires Cid to help rescue Singh, and she sends the Bad Batch; they are reluctant to help after fighting against the Separatists in the Clone Wars. Omega is left behind due to the bounty hunters that are targeting her, and she wins Cid enough money playing dejarik to pay off the Bad Batch's debt. With the help of GS-8, the Bad Batch rescues Singh and take him to Cid for payment. |
| 11 | 11 | "Devil's Deal" | Steward Lee | Tamara Becher-Wilkinson | July 9, 2021 (2021-07-09) |
| When Senator Orn Free Taa announces a new Imperial refinery on Ryloth and encourages Twi'lek freedom fighters to disarm, resistance leader Cham Syndulla publicly supports the Empire. His lieutenant Gobi Glie takes Cham's daughter Hera on a secret mission to retrieve weapons from the Bad Batch, during which Hera befriends Omega. Crosshair tracks them, and the Empire arrests Glie and Hera for treason. Cham attacks the Imperial convoy to rescue them with his wife Eleni and other freedom fighters. Crosshair shoots Orn Free Taa, allowing Rampart to frame Cham for Taa's attempted assassination. Cham, Eleni, and Glie are arrested but Hera escapes. |
| 12 | 12 | "Rescue on Ryloth" | Nathaniel Villanueva | Jennifer Corbett | July 16, 2021 (2021-07-16) |
| Hera contacts Omega and asks the Bad Batch to help rescue her parents. Hunter does not think this is worth the risk, but Omega convinces him. Hera, Omega, Tech, and Wrecker attack the new Imperial refinery on Ryloth as a distraction while Echo and Hunter free Cham, Eleni, and the other freedom fighters. Crosshair discovers this and sets a trap for them, but clone Captain Howzer—who is loyal to Cham—warns the escapees of the trap and then confronts his fellow soldiers. Howzer is arrested while the Bad Batch and freedom fighters escape. Rampart realizes that he has underestimated the Bad Batch and gives Crosshair permission to hunt them down. |
| 13 | 13 | "Infested" | Saul Ruiz | Amanda Rose Muñoz | July 23, 2021 (2021-07-23) |
| The Bad Batch returns from a mission to find Cid's parlor under the ownership of crime boss Roland Durand. They find Cid outside, and she reveals a plan to take back the parlor by stealing a shipment of spice from Roland that is intended for the Pyke Syndicate. The Bad Batch and Cid enter her office via underground tunnels infested with a hive of Irlings. They retrieve the spice, but are chased by Roland's guards who awaken the hive. The group escape from the tunnels but lose the spice to the hive. They are caught by the Pykes, who take Omega hostage while the Bad Batch and Cid retrieve the spice from the hive. The Pykes then let Cid reclaim her parlor. |
| 14 | 14 | "War-Mantle" | Steward Lee | Damani Johnson | July 30, 2021 (2021-07-30) |
| Rex contacts the Bad Batch and asks them to respond to a distress signal from clone commando Gregor on the planet Daro. At the source of the signal, they find an Imperial base where conscripted soldiers are being trained by clone commandos to replace the clone trooper army. Hunter, Tech, and Echo infiltrate the base while Omega and Wrecker stay in the ship as backup. The Bad Batch rescues Gregor, but Hunter is captured during the escape. On Kamino, Lama Su and Nala Se plan to escape after the Empire cancels their clone army contracts, but they are caught by Rampart. He says the Empire has a use for Nala Se as a scientist, but not for Lama Su. |
| 15 | 15 | "Return to Kamino" | Nathaniel Villanueva | Matt Michnovetz | August 6, 2021 (2021-08-06) |
| Hunter is taken to Tipoca City on Kamino, where the Empire has evacuated critical personnel and eliminated the rest. Crosshair activates Hunter's communicator to lure the rest of the Bad Batch there. Omega shows the others a hidden entrance into Nala Se's secret laboratory, where they were all created and where they find the friendly droid AZI-3. They find Hunter, who tries to convince Crosshair to have his inhibitor chip removed, but Crosshair reveals that it has already been removed and he is willingly working for the Empire. Hunter stuns Crosshair as Rampart, under the orders of Tarkin, begins destroying Tipoca City with the Bad Batch and Crosshair still inside. |
| 16 | 16 | "Kamino Lost" | Saul Ruiz | Jennifer Corbett | August 13, 2021 (2021-08-13) |
| Rampart and the Empire depart as the wreckage of Tipoca City sinks into the ocean. Omega and AZI-3 save Crosshair when they are trapped in a flooding room. Once the wreckage of the city settles on the ocean floor, the group make their way to an access tube that leads to the Marauder, but find it damaged. Crosshair suggests AZI-3 guide them to the surface inside lab capsules, but the droid runs out of power on their way up. Omega tries to save him at the risk of drowning, until Crosshair saves them both. When they reach the Marauder, Crosshair chooses to part ways with the Bad Batch. Nala Se is brought to a secret Imperial facility at Mount Tantiss. |