“Infiltration”

The assassination attempt
The episode opens with former Clone trooper Rex escorting the fugitive Separatist Senator Avi Singh and his RA-7 protocol droid GS-8 to a safe house through the streets of a city at night. GS-8 is unsure about the safe house, but Singh replies that they are not safe anywhere. Another former Clone trooper, Howzer, keeps watch from a balcony and corresponds with Greer, who confirms the interior is secure. They are being watched by a Clone assassin, CX-1, from a high tower.

Rex brings Singh and GS-8 inside the hotel for a secret meeting with Imperial Senator Riyo Chuchi. Despite fighting on opposite sides during the Clone Wars, the two senators met to discuss the growing dissent against Emperor Palpatine throughout the former Galactic Republic and Confederacy. Singh warns that they must be cautious since they have no unifying leaders. Chuchi says the Emperor is acting cautiously due to public opinion. Singh counters that such limitations have not stopped the Empire from occupying planets, including his homeworld of Raxus. Singh is still determined to do anything for his homeworld and asks what Chuchi suggests.

Meanwhile, CX-1 navigates through the tunnels and climbs out of a manhole that leads to the hotel. He surprises and chokes Greer with his blaster. Unable to contact Greer, Howzer contacts Rex and tells him to check the kitchen. Rex warns the hotel patrons that there is an intruder. The assassin throws a bomb at the senators, but Rex tosses it out of their room, causing an explosion that blows a hole in the wall. Rex and Howzer pursue the assailant underground.

CX-1 uses the tunnels to flee to the southern maintenance tower. The assassin damages a gas tunnel to slow down his pursuers. Still, at the top of the maintenance tower, it is stunned by another former Clone trooper, who identifies him as a “shadow” they keep running into.

The prisoner
Rex and his former Clone comrades travel on a shuttle through hyperspace with CX-1. Rex advises Senator Chuchi to keep a low profile. Rex and Howzer discuss an object they have recovered from their prisoner. Rex tells Howzer to make arrangements for Fireball to examine the object at base camp, which turns out to be a ruined B’omarr Order Monastery on the planet Teth.

At the base camp, Fireball explains that the object was an electro capsule implanted into the assassin’s teeth. Fireball also notices that his identifying number has been wiped and ponders what the Empire did to him. When CX-1 awakes, Rex speaks to him, saying he is still one of them despite what the Empire has done to him. The prisoner remains silent.

Meanwhile, at Tantiss Base, Commander Scorch activates a Clone assassin and explains that CX-1 has been compromised due to his capture. He orders the Clone assassin to track down CX-1 and neutralize him.

Elsewhere, CX-1 remains silent but briefly nods when Rex asks if he is from Mount Tantiss. Rex asks where Tantiss is located, and CX-1 remains silent. Howzer tells Rex to push the prisoner harder. Fireball interrupts and informs Rex and Howzer that CX-1’s data puck was a target register. Fireball says that CX-1’s targets included Singh and Omega. Rex orders Fireball to contact Echo and Hunter immediately.

Howzer thinks the Bad Batch can help, but Rex is unwilling to involve them. However, Howzer thinks Crosshair can help them and believes that CX-1 can help reveal Tantiss’s location.

Reunion with Rex
While the Bad Batch travels aboard the Marauder through hyperspace, Echo tells Hunter he is taking them to a secret base. When Hunter asks about his rendezvous with Gregor, Echo replies that he will pick him up after dropping the rest of the team off at the base. Echo cannot explain why Rex wants to see them but says it is important.

The Bad Batch disembarks outside Rex’s base on Teth, where Rex and Howzer greet them. Rex is pleased to see Omega, but Howzer is unhappy to see Crosshair, with whom he still has unfinished business on Ryloth. Rex reassures Howzer that Crosshair is now on their side. Before leaving, Echo hands Omega an energy crossbow, which he obtained from some interesting contacts in the galaxy. He tells Echo he won’t be long and jokingly tells her to keep the others in line.

The Clone Underground
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 is 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 is 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 of the project’s purpose 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.

Secrets of Tantiss
The clone assassin climbs the mountain where Rex’s base camp is situated and plants remote-controlled explosives on several ships and structures. Omega tells Rex that more clone prisoners are on the base, and Rex promises to get them out. Fireball serves a meal based on Gregor’s recipe with some spicy modifications. Before settling for the meal, Crosshair reveals that not all the Clones on Tantiss are prisoners, and some remain loyal to the Empire.

He explains that a special Clone division is trained as specialized operatives and initiated into a deep cover program by Dr Royce Hemlock. He explains that their identities are erased and that they are reconditioned. The few who survive the program come out differently. 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 deep-cover 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 uses a special tracker to elude their scanners. He warns them not to underestimate Hemlock.

Hunters of the Empire
Meanwhile, the second clone assassin infiltrates the base, moving past Omega and Wrecker in the mess hall. The assassin sees Omega and considers targeting her before changing his mind. Batcher senses movement, but Omega thinks he is hungry, so he gives him her bowl. Outside the base, the clone assassin informs Wolffe that Omega is present with a group of rogue clones at the base. Wolffe 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 explosions tear through the base, disabling comms. CX-1 laughs defiantly before he guns him down. The rogue clones engage in a gunfight with the intruder. Rex tells Nemec to restore communications, but the assassin removes 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 led by Commander Wolffe approach Teth. He orders his troops to set their blasters to stun and bring the prisoners back alive.