"Infiltration" marks the sixth installment of the third season of Star Wars: The Bad Batch. This episode was released on March 13, 2024, simultaneously with the seventh episode.
The episode commences with Rex, a former Clone trooper, escorting Avi Singh, a fugitive Separatist Senator, and his RA-7 protocol droid, GS-8, through a city's nighttime streets toward a safe house. GS-8 voices concerns about the safe house, but Singh asserts that nowhere is truly safe for them. Howzer, another former Clone trooper, is positioned on a balcony, communicating with Greer to confirm the interior's security. Unbeknownst to them, CX-1, a clone assassin, observes them from a tall tower.
Rex guides Singh and GS-8 into the parlor for a clandestine meeting with Riyo Chuchi, an Imperial Senator. Despite their opposing allegiances during the Clone Wars, the two senators convene to address the growing resistance against Palpatine, the Emperor, across both former Galactic Republic and Confederacy territories. Singh cautions that their lack of unified leadership necessitates vigilance. Chuchi notes that the Emperor is acting cautiously due to public sentiment. Singh retorts that such constraints have not prevented the Empire from occupying planets, including his home planet of Raxus. Singh remains steadfast in his commitment to his homeworld and inquires about Chuchi's proposal.
Simultaneously, CX-1 navigates the tunnels, emerging from a manhole leading to the parlor. He ambushes and subdues Greer with his blaster. Unable to reach Greer, Howzer alerts Rex and instructs him to inspect the kitchen. Rex warns the patrons of an intruder. The assassin hurls a bomb at the senators, but Rex throws it out of the room, resulting in an explosion that breaches a wall. Rex and Howzer pursue the attacker underground.
CX-1 escapes through the tunnels toward the southern maintenance tower. He slows down his pursuers by damaging a gas tunnel but is ultimately stunned atop the maintenance tower by another former Clone trooper, who identifies him as a recurring "shadow."
Rex and his former Clone allies transport CX-1 aboard a shuttle through hyperspace. Rex advises Senator Chuchi to maintain a low profile. Rex and Howzer discuss a heavily encrypted data puck recovered from their prisoner. Rex instructs Howzer to arrange for Fireball to analyze the object at base camp, which is revealed to be a dilapidated B'omarr Order Monastery on the planet Teth.
At the base camp, Howzer explains that the object was an electro capsule implanted in the assassin's teeth. Howzer also observes that his identifying number has been erased, prompting him to contemplate the Empire's actions. Upon CX-1's awakening, Rex addresses him, emphasizing that he remains one of them despite the Empire's manipulations. The prisoner remains silent.
Meanwhile, at Tantiss Base, Commander Scorch activates CX-2, another clone assassin, explaining that CX-1 has been compromised due to his capture. He tasks the Clone assassin with locating and eliminating CX-1.
Elsewhere, CX-1 maintains his silence but offers a subtle nod when Rex asks if he originates from Mount Tantiss. Rex inquires about Tantiss's location, but CX-1 remains unresponsive. Howzer urges Rex to exert more pressure on the prisoner. Fireball interrupts, informing Rex and Howzer that CX-1's data puck contained a target register. Fireball reveals that CX-1's targets included Singh and Omega. Rex orders Fireball to immediately contact Echo and Hunter.
Howzer suggests that the Bad Batch could assist, but Rex is hesitant to involve them. However, Howzer believes that Crosshair could provide valuable assistance and potentially reveal Tantiss's location.
As the Bad Batch travels aboard the Remora through hyperspace, Echo informs Hunter that he is taking them to a secret base. When Hunter inquires about his rendezvous with Gregor, Echo replies that he will pick him up after dropping the team off at the base. Echo is unable to disclose the reason for Rex's request but emphasizes its importance.
The Bad Batch disembarks outside Rex's base on Teth, where they are greeted by Rex and Howzer. Rex expresses his delight at seeing Omega, but Howzer is displeased to see Crosshair, with whom he still has unresolved issues stemming from Ryloth. Rex assures Howzer that Crosshair is now on their side. Before departing, Echo hands Omega an energy crossbow, acquired from contacts within the galaxy. He tells Echo that he won't be long and tells her to keep the others in line jokingly.
Meanwhile, the clone assassin lands his starship in a nearby forest clearing on Teth and disembarks his ship. He follows CX-1's implant beacon. Inside his base, Rex introduces other members of the Clone Underground and tells the Bad Batch of his plan to rescue their Clone brothers from Tantiss Base. Rex tells Hunter that he recovered a target list from an Imperial operative that includes Omega. Crosshair says that Omega is a target because she escaped Imperial custody. When Howzer asks Crosshair why he is not on the list, Crosshair thinks he is not important.
When Howzer accuses Crosshair of being a traitor, Hunter warns him to back down. Howzer questions whether Crosshair was a captive and his assertion that he doesn't know the base's location. Crosshair responds that he is telling the truth. Crosshair says he has broken with the Empire but Howzer does not believe him. When Omega enters the room with Batcher and Wrecker, Crosshair tells her that the Empire is targeting her again. Wrecker says he is not surprised.
When Rex asks Omega why the Empire was interested in her, Omega explains that the Empire was using her as a hostage to force Nala Se to cooperate in certain experiments. Omega adds that Nala Se was working on a project involving M-Count. She is unaware about the purpose of the project but explains that they were taking blood samples from all the Clone prisoners including her. Rex has heard about M-Counts but is unsure what it is about. Rex asks Omega to tell her more.
The clone assassin ascends the mountain where Rex's base camp is located and plants remote-controlled explosives on various ships and structures. Omega informs Rex that there are more clone prisoners on the base and Rex promises to get them out. Fireball serves a meal, which is based on Gregor's recipe with some spicy modifications. Before they settle down for the meal, Crosshair reveals that not all the Clones on Tantiss are prisoners and that some are still loyal to the Empire.
He explains that there is a special Clone division who are trained as specialized operatives and initiated into a deep cover program run by Dr. Royce Hemlock. He explains that their identities are erased and that they are reconditioned. The few who survive the program come out different. When Howzer asks Crosshair how he knows so much about the program, Crosshair explains that the Imperials tried to make him into one of these assassin clones. Crosshair failed the program since being defective is his nature. Hunter recalls they encountered one of these Clone operatives on Coruscant earlier.
When Hunter asks what Rex is keeping from them, Rex explains that they captured a Clone assassin. Crosshair expresses surprise to learn that they have a Clone assassin prisoner and warns that the Empire tracks their operatives. When Howzer responds that they have scanned the prisoner, Crosshair warns that the Empire is using a special kind of tracker that is undetectable to their scanners. He warns them not to underestimate Hemlock.
Meanwhile, the second clone assassin infiltrates the base, moving past Omega and Wrecker in the mess hall. The assassin sights Omega and considers targeting her before changing his mind. Batcher senses movement but Omega thinks he is hungry and gives her her bowl. Outside the base, the clone assassin informs Scorch that Omega is present at the base with a group of rogue clones. Scorch orders the assassin to send the coordinates and to prepare for the Recovery Strike Team. He then issues orders for the girl to be taken alive.
The Bad Batch and Rex confront CX-1, who recognizes Crosshair. Crosshair warns them to leave but CX-1 claims that Crosshair has information he is hiding from the others. CX-1 warns the others that the Empire is coming for them just as a series of explosions tear through the base, disabling comms. CX-1 laughs defiantly before he is sniped by the assassin. The rogue clones engage in a gunfight with the intruder. Rex tells Nemec to restore communications but the assassin takes out Nemec and the backup generator.
The Bad Batch and Omega retreat into the command room while Rex and his clones fight the intruder. Fireball deploys a flamethrower but the assassin shoots him. The flamethrower activates a thermal detonator, which causes a cave-in that destroys the mess hall. Rex manages to escape into the command room.
In space, two shuttles carrying Clone Commandos and TK stormtroopers led by Commander Wolffe approach Teth. He orders his troops to set their blasters to stun and bring the prisoners back alive.