The fugitive
The episode opens with a wide shot of a mountain landscape followed by forests on the planet Daro. A Clone trooper is being pursued through the forest with search lights by a pack of massiffs, who are controlled by other Clone troopers. The Clone trooper reaches the edge of a cliff and is forced to turn a corner. The fugitive is cornered by two massiffs. Before fleeing into the forest, he plants a beacon which glows. The Clone trooper flees into a field covered by ferns but is stunned twice. The Clone trooper is then taken prisoner by his fellow clones.

Answering a friend’s call
While the Havoc Marauder travels through hyperspace, Omega fixes Gonky while Hunter fingers a knife. Echo informs them that they are being hailed by Rex. When the Bad Batch gather in the bridge, Rex tells them that he needs their help and explains that he received a distress signal from a Clone trooper. However, he is a bit tied up right now to retrieve him. Hunter asks if he wants them to recover another “regular trooper.” Rex explains the Clone trooper is an old friend who is in trouble and that he needs them to get him out. Before Rex can explain, a beacon rings and he says he has to go now. Rex instead transmits the coordinates to the Bad Batch.

When Wrecker asks what that was all about about, Tech explains that the distress signal sent by CC-5576-39 originated from Daro, a terrestrial planet in the Outer Rim Territories with no known settlements or installations. Hunter asks what he is doing all the way out there. Echo asks if it matters. Hunter explains that they have gone on missions before without much intelligence but that this would be stretching it. Echo responds that Rex wouldn’t be asking for help if it wasn’t urgent. Wrecker agrees but Tech reminds them that they are traveling on a job for Cid. He says that if they deviate, they won’t be compensated. He adds that they need the money to buy food.

Wrecker agrees with Tech but Omega points out that Wrecker’s friend is in trouble and that is more important than getting paid. Wrecker says that Omega has a point. After a hard stare from Echo, Hunter reluctantly agrees to check things out but says that he doesn’t like.

A looming storm
At Tipoca City on Kamino, Crosshair tells Vice Admiral Rampart that the operation is ahead of schedule. A pleased Rampart asks that every available Clone be mobilized. As Low Altitude Assault Transport/infantry gunships takeoff, a Kaminoan watches. When Crosshair asks about the Kaminoans, Rampart says that they have their orders and to keep their eye on them till the time is right.

Elsewhere in the facility, a group of juvenile clones are preparing to disembark. One of them asks Mistress Nala Se if leaving the facility is against protocol. She tells them that their training will continue elsewhere. The young clone asks if they will still be soldiers. She reassures them that this is what they were made for. She tells the clones to hurry while she speaks with Prime Minister Lama Su.

Lama Su leads Nala Se to a private room where he tells her that the Galactic Empire has canceled all their contracts. Nala Se that their success with the Grand Army of the Republic is known galaxywide and hopes that they will find other clients who will value their scientific advancements. Lama Su responds that the Empire is not like the Galactic Republic and that they have empowered them to their own detriment. He fears that the Empire will destroy them rather than allow their cloning operations to continue. Lama Su says that they must leave to ensure their survival. He orders her to gather those essential while he makes arrangements for their departure. Nala Se agrees.

Planetfall
The Havoc Marauder descends into Daro’s atmosphere. Tech brings the ship low to avoid being detected by scanners. Hunter is skeptical about banking a lot on a clone they do not know. Echo says that Rex trusts the Clone and that he trusts Rex. The Havoc Marauder lands in a forest clearing and the clones disembark. Tech uses a device to home in on the beacon’s signal. Omega finds the beacon under a fern.

Wreckers asks about this regular. Examining the forest floor, Hunter realizes that the clone fugitive was hunted and being dragged. The Bad Batch and Omega follow his trail, which leads towards a mountain. Hunter deduces that there is something inside the mountain. Tech agrees and says that something is jamming his scanner. When Wrecker reminds Tech that he said that nothing was on the planet, Tech says that data appears to be inaccurate.

Despite Omega’s objections, Hunter tells her and Wrecker to stay aboard the Havoc Marauder. Hunter leads the other clones towards the mountain. While examining the trail, Hunter finds that a shuttle has landed at the base of the mountain. When Echo asks what is inside the mountain, Hunter replies that their is only one way to find out. The clones hike up the forested mountain and reach the top, which overlooks a subterranean secret military base. The clones duck as a shuttle flies over them and lands inside the base.

Descending down the hill, the clones navigate their way through the base facilities. Using a pair of macrobinoculars, Echo discovers a couple of Clone commandos and stormtroopers standing at attention. He notices that the “clones” are wearing updated armor. While Hunter borrows the macrobinoculars, Tech explains that mountain’s natural composition makes this base well-fortified and nearly impenetrable. As more stormtroopers descend from the shuttle, Hunter says that this is no longer a simple extraction and thinks that they should return to the Marauder and leave word for Rex.

Into the base
When Echo reminds them of the mission, Tech responds that they do not know for certain if CC-5576 is even in there or if he is still alive. Hunter adds that they will be going in blind without reinforcements. Echo points out that the Bad Batch did that when they rescued him on Skako Minor and that he would still be trapped there if they hadn’t. Echo says that if there’s a chance that the Clone trooper is being held there against his will, they have to try and get him out.

Aboard the Havoc Marauder, Omega and Wrecker are playing at taking turns when they receive Hunter’s transmission. Hunter tells them that they have not found the “regular” yet but that they have found an Imperial base built inside the mountain. He tells them that they are going in. Omega wants to help but Hunter reminds them of their orders to stay aboard the ship to provide back-up. He adds that comms will be jammed once they are inside and tells Omega and Wrecker to stay on alert.

Tech says that he will need to tap into the central database to pinpoint CC-5576’s location. Echo suggests entering the base through entry points in the lift shaft. The three clones jump on top of a turbolift and enter the base through an elevator shaft. Inside the base, Echo uses his cybernetic arm to access a network terminal. He finds that the encryption is new. The Clones hide while a squad of troopers wearing the new armor walk past and enter a lift.

While reading the muster report, Echo finds that it lists 50 clone commandos and 1,000 TK troopers. Tech is unfamiliar with the new designation. Hunter asks about progress and Echo finds that the prisoner is in Cellblock 25, which is four levels down. The three clones descend deeper into the base.

Prison break
Inside his cell, “Gregor” demands that his captor bring him food. The guard dismisses him as a traitor but “Gregor” reminds him that he is “Captain Traitor.” Just then, the Bad Batch knock out the guard. Echo asks if he is CC-5576. Hunter explains Rex sent them. Gregor tells them that his name is Gregor and accepts his rescuers’ help. Traveling through the corridors, the Bad Batch and Gregor seek to avoid the other Clone troopers.

Gregor explains that the troopers have gathered for inspection and that there is no way past them. Echo points out that if they can’t reach the lifts, they can’t get out. Tech says that he can redirect them and heads to a network terminal. When Gregor asks if they are Clone Commandos, Hunter explains that they are CT-99s, the so-called “defectives.” Gregor quips that the Clone troopers who are loyal to the Empire are the real defective clones. When Echo asks what was Gregor’s assignment, he explains that he was an instructor.

Just then, klaxons ring. Tech explains that he keyed a Code-16 to redirect their forces. Gregor explains that clone codes don’t work here and that he just triggered a security alert. The clones are attacked by Imperial storm troopers and a blaster battle rages. The Clones stun some of them with Hunter breaking the neck of one of his opponents. When Hunter asks if there is another way off the base, Gregor says that the only way out of the base is up.

Examining the body of a fallen stormtrooper, Tech realizes that these are not clone troopers. Gregor explains that these are their “replacements.” Hunter stuns a pursuing stormtrooper and uses a stun grenade to take out more stormtrooper reinforcements. The Bad Batch fight their way through the stormtroopers. Tech asks Gregor if he is sure that he knows where they are going. Gregor replies that he escaped before but Tech reminds him that was captured. Gregor counters that was after he made it out.

When Hunter asks if Gregor had trained these new stormtroopers, Gregor replies that he didn’t teach them everything since that wouldn’t have been smart. The clones reach an elevator shaft. They stun the occupants and drag them out. Tech uses an authorization code to activate the lift, which rises to the top of the mountain.

When Echo asks about the new “replacement” troopers, Gregor explains that the Clone troopers were soldiers of a Republic that no longer exists and that these new recruits come from all over the galaxy. He says that they swear loyalty to the Empire. While they are not as skilled, there is an endless supply of them. Hunter replies that numbers are not everything. When they reach the top, they are confronted by a squad of stormtroopers. The clones are force to take the lift down for a “detour.”

Change of plans
Back at the Havoc Marauder, Gonky walks around while Wrecker rests. Omega asks how Wrecker can be so relaxed. Wrecker says that he is “charging” before the action. Omega is worried that they haven’t heard from the rest of the Bad Batch and thinks that something has gone wrong. Wrecker thinks they have everything under control.

Meanwhile, the Bad Batch and Gregor engage in a blaster battle with stormtroopers, stunning several. Hunter jumps on top of a lift before grabbing part of the lift shaft. Tech and the others stun a Clone Commando named Scorch. Gregor is wounded during the shooting. He, Wrecker and Tech seek shelter in a control room and disable the door controls. Gregor makes light of his wounds. Hunter joins them and says that the Imperials have blocked off all entry points to the main ring.

Tech proposes using reactor conduits to escape the base. Gregor points out that the exhaust vent is halfway up the mountain and that they can’t survive that jump. Tech says that they can signal their ship Havoc Marauder for a pick-up. He blows open the hatch leading to the reactor conduit. While traveling through the conduit, Echo asks Gregor how he ended up on Daro. While coughing, Gregor says that he was sent here with other Clone commandos but quickly realized that he wanted out. Gregor quips that the Empire does not take kindly to desertion.

Meanwhile, Omega waits on the gangplank of the Havoc Marauder. Hunter contacts Wrecker and Omega, telling him that they found the target but need a pick-up because they ran into trouble. Wrecker and Omega lift-off in the Havoc Marauder. Meanwhile, the stormtrooper patrol realizes that the fugitives are escaping into the reactor port. The Bad Batch and Gregor reach the reactor port as the Havoc Marauder approaches. In response, several LAAT gunships and V-wing starfighters depart from the base.

The Bad Batch and Omega find themselves under attack from behind. Under Wrecker’s guidance, Omega manages to pilot towards the reactor conduit. Wrecker extends the gangplank so that the clones can cross. Before they can complete the evacuation, the Havoc Marauder is attacked by several V-wing starfighters. Tech and Gregor manage to board the ship. Tech takes control of the ship and assigns Wrecker to the rear gun. The Havoc Marauder leads the V-wings on a chase.

Hunter’s choice
Meanwhile, Hunter and Echo fight with the stormtroopers. During a struggle with Hunter, one of the stormtroopers falls over the edge. Wrecker manages to take down two V-wings but the ship’s shield generator is damaged during the dogfight. Omega tells Gonky they need him and plugs the droid up to the ship’s power system, restoring the deflector shields. This allows Tech to circle the mountain base long enough for Wrecker to shoot one of the V-wings, causing it to collide with another one. Tech tells Echo and Hunter that they are coming back and to be ready.

Echo manages to jump aboard. However, more V-wings arrive, disrupting their rescue. Hunter jumps and attempts to reach the gangplank but loses his grip and falls down the hill into the forest. He manages to break his fall with his knife. Omega screams in despair. Back in the cockpit, Gonky experiences a short-circuit and the ship experiences multiple system failures. The Havoc Marauder manages to take out a couple of V-wings with its rear cannons.

Meanwhile, an LAAT gunship lands near Hunter. Hunter rises to his feet and tells the other clones to save themselves and get out of here. Tech is unwilling to abandon Hunter but Hunter orders him to take the others to safety. As the Havoc Marauder rises into the skies, Wrecker continues exchanging fire with the pursuing V-wings. Several crash into the mountain while others are shot down. Omega pleads with Hunter to order the rest of the Bad Batch to turn around but Hunter is unwilling to sacrifice his team to save himself. He allows himself to be captured by stormtroopers. The Havoc Marauder flees into hyperspace.

Imperial captivity
At Tipoca City, Vice-Admiral Rampart confronts Prime Minister Lama Su, telling him that he is disappointed at the Kaminoans’ lack of cooperation. He informs the Prime Minister that a disturbing matter has been brought to his attention. As Elite Squad Troopers enter the room with Nala Se, Rampart says that Su’s Chief Scientist was gathering medical personnel to flee Kamino. Lama Su feigns surprise and says he will decide on a suitable punishment.

Rampart says that while he found the Clone troopers overrated, he tells Nala Se that he hopes to utilize her services for the Empire. However, he has little need for Lama Su’s services. Two Elite Squad Troopers take the Kaminoan Prime Minister into custody.

Back on Daro, Hunter is locked in a cell. He is greeted by his former comrade Crosshair, who says he was hoping for the whole squad but is satisfied with Hunter for now.