The hundredth episode of the animated series, and the twelfth from Star Wars: The Clone Wars' fifth season, is titled "Missing in Action". It was originally broadcast on January 5 of 2013.
D-Squad has made its way to the shady settlement of Pons Ora. While the astromech droids scout the area for potential threats, Colonel Gascon and WAC-47 step into a local eatery seeking sustenance. However, upon announcing their presence, they are impolitely ejected by the diner's cook, Borkus. WAC directs Gascon to the side of the establishment where a multitude of insects are converging on the discarded food. Despite his aversion to the idea of consuming leftovers, Gascon sees no other option. Before he can indulge, however, a human dishwasher called Gregor emerges from the diner to dispose of the trash, inadvertently striking Gascon. Offering an apology, Gregor volunteers to provide him with some food on the house. Gascon, however, fixes his gaze upon Gregor and identifies him as a clone trooper. Gregor appears to be completely unaware of what a clone is and is subsequently called back to his duties. Gascon and WAC then rejoin the astromech droids, who have confirmed the presence of Separatist forces on Abafar.
Once his shift concludes, Gregor inquires of Borkus regarding the nature of a clone. The Sullustan provides a vague explanation, stating that clones participate in a galactic conflict, and advises Gregor to disregard the matter, reminding him that he was the one who discovered him. Despite Gregor's gratitude for his assistance, he questions how he came to be on Abafar. Borkus evades the question, instructing Gregor to return home and to never utter the word "clone" again.
Concurrently, D-Squad discovers a heavily fortified landing zone containing a Rho-class transport shuttle. Although Gascon insists on a discreet approach to the shuttle, the droids suggest that the Separatists may be actively searching for them following their escapade on the dreadnought. Recognizing that a direct assault would be tantamount to suicide, Gascon opts to seek Gregor's assistance.
D-Squad locates Gregor's residence and captures his attention by having R2 project a holographic image of Captain Rex. They reveal to him his true identity as a clone, destined to fight for the Republic. Gregor expresses reluctance to believe them, stating that he is fortunate that Borkus is covering his rent. Gascon clarifies that he is essentially Borkus' indentured servant. Given Gregor's amnesia, Gascon directs R2 to scan the identification code on Gregor's wrist, which reveals him to be a commando clone. He had been officially listed as missing in action during the Battle of Sarrish, a particularly devastating military setback for the Republic. Experiencing fragmented recollections of the battle, Gregor consents to aid D-Squad. They then embark on a search for his equipment, unaware that Borkus is observing them. They proceed to Borkus' diner, only to have the Sullustan approach them, revealing that he possesses Gregor's gear. Gregor demands an explanation for why he concealed the truth from him. Borkus replies that he was indifferent and reminds Gregor that he owes him a life debt. The clone counters that he turned him into a slave and demands his equipment. Borkus gains the upper hand on Gregor, but the droids restrain him. As D-Squad prepares to depart, Borkus implores Gregor not to abandon him, but he refuses. Borkus then discloses that the Separatists intend to detonate a Republic cruiser in orbit using the rhydonium fuel they have been mining. He asserts that they will never escape and will be begging him for employment.
D-Squad returns to the landing zone, confirming the veracity of Borkus' information. D-Squad collectively agrees to rescue the cruiser. Gregor provides covering fire for Gascon and the droids as they advance toward the shuttle. However, battle droids detect D-Squad and unleash a barrage of fire upon them. A stray projectile strikes a Rhydonium canister, causing BZ and Gascon to fall inside. The Colonel instructs WAC to abandon him, an order that the pit droid promptly obeys. However, Gregor returns to retrieve him and remains behind to provide cover for their escape. Despite Gascon and R2's insistence that they can rescue him, Gregor assures them that he will eventually return home. As the Separatists encircle him, Gregor detonates nearby canisters, triggering a series of massive explosions. As their shuttle departs Abafar, Gascon vows that Gregor's sacrifice will be remembered and that they will await his return.
Originally, Star Wars Insider 137 reported "Missing in Action" as the eleventh episode of Season Five. However, this placement was later corrected after the magazine's release.

In homage to R2-D2, the episode's opening logo, which is normally yellow, was rendered in blue. This blue logo is also present in the other three episodes of this droid-centric storyline: "Secret Weapons," "A Sunny Day in the Void," and "Point of No Return." However, this is not the first instance of the logo's color being altered. In the final two episodes of Season 4 - "Brothers" and "Revenge" - the logo was colored red to signify the return of Darth Maul.