"The Final Conflict" represents the sixth installment within the animated television show Star Wars Rebels, specifically from its third season. As the series' forty-third episode overall, it was broadcasted on October 22, 2016 via Disney XD.

The episode commences with the rebel freighter Ghost entering the atmosphere of the planet Agamar. The Ghost touches down near the wreckage of a former Separatist supply ship. The Spectres in conjunction with Captain Rex exit the vessel. When Hera Syndulla inquires about potential complications, Kanan Jarrus jokingly anticipates a disastrous outcome. Ezra Bridger assures her of their safety due to Rex's presence. Subsequently, the Ghost departs into space with Hera and Sabine Wren on board.
Rex then clarifies to Kanan, Ezra, and Garazeb Orrelios that a battle transpired on Agamar during the Clone Wars, emphasizing that the destroyed Separatist transport is an ideal location to procure ammunition, notably proton bombs. Upon Ezra's query about encountering battle droids, Rex informs him that the transport ship was once teeming with "clankers." Zeb questions Rex about the quantity of battle droids he eliminated. Rex approximates that he annihilated thousands, possibly tens of thousands, but did not maintain a precise count, unlike some other Clone troopers.
Ezra picks up a B1-series battle droid's head, suggesting that the droid appears harmless. Rex counters by stating that these "clankers" were responsible for the deaths of numerous Republic soldiers during the Clone Wars, including several of his comrades. Kanan adds that battles inflict lasting wounds, some of which are invisible. The rebels then proceed through the transport's munitions depots. Rex confirms that they are fully stocked with proton bombs. Simultaneously, Chopper detects multiple operational B1 battle droids uttering "Roger Roger."

Later, Rex and his team find themselves confined within a ray shield, a technology employed by the Separatists to safeguard their battle droids. Ezra then observes that they are encircled by a multitude of battle droids. A battle droid commander, designated B1-268, announces that they have been captured by the Separatist Alliance and instructs his subordinates to eliminate the Republic "invaders." However, B1-268 subsequently receives revised orders to stun and apprehend the intruders. Ezra then inquires about the meaning of the call sign "Roger Roger." B1-268 directs his troops to escort the prisoners to the command center. Unbeknownst to the droids, Chopper is monitoring them using his camera. B1-268 then remarks that they have never captured anyone previously. The rebels are incapacitated by a stun ray.
Subsequently, Rex awakens at the Separatist command center on the bridge of the wrecked transport. He discovers that he is a prisoner of a super tactical droid named Kalani, who acknowledges B1-268 for his efforts. Rex experiences flashbacks of the Clone Wars and utters the name of his former comrade Cody. However, Kanan redirects him to the present and informs Rex that their captor is a super tactical droid. When Ezra questions if this is a negative situation, Rex affirms that it is due to the super tactical droid's intelligence.
Kalani then addresses the rebel prisoners, noting that the Separatist Droid Army outnumbered the Grand Army of the Republic to such an extent that he calculated their probability of defeat at 23.8%. When Rex asks Kalani why he remains operational despite Order 66, the super tactical droid explains that he bypassed the command signal on Agamar, suspecting it to be a Republic ruse. Rex asserts that the Clone Wars are concluded, irrespective of Kalani's beliefs, and demands his release.
Kalani declines his request, asserting that this is an opportune moment to conclude the war with a Separatist Alliance victory. Kalani intends for his prisoners to engage in combat to substantiate his hypothesis that the Separatists had a greater likelihood of victory than the Republic and Jedi. When Zeb objects to participating in Kalani's war game, the tactical droid concurs with the Lasat on the basis that his species was not involved in the Clone Wars. Instead, he designates Zeb as the hostage that the other rebels must rescue in a rescue simulation based on 132 Clone Wars battles. Kanan and Rex decline to fight, but Ezra insists that they accept this challenge as a game. Subsequently, Kanan and Rex reconsider their decision. Ezra also stipulates that Kalani release Zeb and provide them with all of the proton bombs if they prevail in the exercise. Kalani accepts Ezra's terms.

Upon Kalani's command, B1-268 announces that the commander has initiated Battle Plan Zeta and instructs the other B1 battle droids to assume their positions. Chopper spies on the battle droids and boards a Neimoidian escort shuttle, which he begins to reactivate. Meanwhile in space, Hera and Sabine are piloting the Ghost, which is being pursued by three TIE fighters. Sabine anticipates that Kanan and Ezra are expecting their return to Agamar imminently. Neither has received communication from their rebel comrades but assume they will contact them if assistance is required.
Elsewhere, aboard an Imperial Star Destroyer, Agent Kallus congratulates Governor Arihnda Pryce on her strategy to ensnare the rebels at a fuel depot. Pryce responds that their plan will only succeed if they manage to capture them. Admiral Kassius Konstantine then reports that they have intercepted an encrypted distress signal originating from Agamar. Pryce finds it peculiar that the rebels would encounter difficulties but issues orders for the nearest Imperial outpost to dispatch troops to Agamar immediately.
Returning to Agamar, Kalani outlines the rules of engagement: the rebels must fight their way back to the command center to liberate Zeb. Rex agrees to spearhead the assault, leveraging his Clone Wars experiences, and proposes attacking the unguarded hangar to surprise the droids. The battle commences upon Kalani's orders, and a column of B1 battle droids engages the three rebels. Kanan instructs Ezra to execute the Sword and Shield maneuver, which involves deflecting blaster bolts and launching grenades at the advancing droid columns. Implementing their strategy, the rebels advance after breaching the initial assault wave. Rex advises Ezra to maintain cohesion as they proceed into the hangar.
Ezra observes that the hangar is clear and suggests entering. However, Rex advises against it, explaining that the battle droids' tactic is to maintain forward momentum and instructs the rebels to wait. Kanan responds that the tactical droid has had ample time to strategize. Rex comprehends the significance of this to Kalani's programming, as well as his own. Rex elucidates to his Jedi comrades that Clone troopers were bred for combat. Together, Rex and the Jedi enter the hangar. Meanwhile, Zeb attempts to persuade Kalani to surrender, but the super tactical droid retorts that he was not programmed to comprehend his sense of humor. Kalani then reveals that the rebels have taken his "bait" and dispatches several droidekas to intercept them.
Unable to penetrate the droideka's deflector shields, Rex and the Jedi are compelled to retreat. Ezra devises a plan to collapse the catwalk onto the droidekas. Kanan and Rex agree to provide covering fire while Ezra proceeds towards the catwalk. Meanwhile, Kalani notes that the Jedi have separated, as they do 76% of the time, and dispatches additional battle droids to pursue Kanan and Rex. Simultaneously, Ezra encounters Chopper, who informs him that he has transmitted a distress signal. Chopper attempts to pull Ezra into the Neimoidian shuttle, but Ezra insists that he will not leave without Rex, Zeb, and Kanan. Ezra instructs Chopper to prepare the shuttle while he retrieves the others.
Ezra's delay frustrates Kanan and Rex, who are under fire. Rex attempts to move but is struck by a battle droid. Meanwhile, Ezra utilizes the Force to collapse the catwalk onto the droidekas. Kanan confirms that Rex is unharmed due to his Clone trooper armor, and they continue towards the command bridge. En route, they encounter Ezra. When Ezra remarks that he would make a capable soldier, Rex points out that their plan relied on precise timing and reprimands Ezra for his tardiness. When Ezra attempts to explain that Chopper wanted to show him something, Rex cautions Ezra that this is not a game and that his every action affects everyone. He emphasizes the need for discipline and strategy. Kanan advises Ezra not to take Rex's words personally, as Rex is determined to conclude the battle.

During their journey, the rebels encounter another droideka, which Rex disables with his helmet following a brief struggle. Rex then observes that the droideka is as antiquated as he is. Kanan checks on Ezra, who confirms that he is unharmed. Rex and the rebels breach the command center and declare victory, with Rex destroying the E-5 blaster rifle Kalani was aiming at them. However, Kalani disagrees and prepares to execute Zeb at gunpoint. Nevertheless, Ezra intervenes and points out that the droid army is so antiquated that they could never have prevailed. While Kalani listens, Ezra contemplates the reasons for the Clone Wars' rapid conclusion.
While Kalani struggles to respond, Zeb explains that the Galactic Empire is the reason for the Clone Wars' cessation. Zeb then indicates that the Empire has arrived in the form of landing craft. The droids and rebels then stand down while Ezra asks Kalani how the droid army will fare against the Empire. Kalani concedes that his droid army is depleted but emphasizes that they are not at war with the Empire. Kalani then directs B1-268 to analyze the approaching Imperial forces. Two Imperial landing craft land near the transport ship and deploy several stormtroopers. B1-268 and his force attempt to greet the Imperials but are attacked. B1-268 himself is crushed by an AT-AT walker, deployed by a landing barge.
In light of the recent events, Ezra argues that the rebels and droids share a common adversary. Rex is about to interject, but Kanan advises him to allow the boy to continue. Ezra then informs Kalani that the conflict between the droids and clones enabled the Empire to seize control. When he asks Kalani what the Separatists were fighting for, the super tactical droid replies that they were fighting for freedom against the Republic's tyranny. Ezra points out that he and his fellow rebels have consistently fought against tyranny. Based on Ezra's words, Kalani infers that the Empire is the successor to the Republic and accepts the logic that this renders the rebels allies.

However, Kalani acknowledges that his forces are diminished and that they have a low probability of success given the overwhelming odds. Kanan offers assistance to Kalani and the battle droids. Ezra then contacts Chopper via comlink, who informs him that the Empire is present. Ezra inquires about the progress with the Neimoidian shuttles. Kalani expresses concern that the Empire will destroy their shuttles. When Kanan asks about the proton torpedoes, Kalani explains that he did not deploy them due to his forces' lack of laser cannons to launch them.
Rex then proposes a plan to roll the proton torpedoes onto the feet of the advancing AT-ATs and AT-DP walkers. Given the battle droids' poor marksmanship, Kalani suggests that the battle droids fire at Ezra and Kanan. The two Jedi will then utilize their lightsabers to redirect the blasts at the proton torpedoes. Subsequently, the battle droids will attack. Kanan instructs the battle droids to prepare the munitions for deployment.
Meanwhile, the Imperial walkers advance towards the hangar. Before preparing for battle, Rex remarks that this is the final glorious day for the Grand Army of the Republic as he observes the Imperial walkers. Ezra instructs Chopper to prepare the shuttles. He also orders D Squad to prepare for their assault. Kalani admits to never attempting such a desperate strategy, prompting Rex to state "that's why we [the Clone troopers] always won." Kalani then replies "not always." Ezra then instructs the battle droids to evacuate on their shuttles once the shells have detonated.
Zeb throws a grenade that disables an advancing AT-DP walker. Zeb joins battle droids and droidekas in the attack while other droids roll the proton torpedoes. Implementing their plan, Kalani orders his droids to fire at Ezra and Kanan, who then deflect the blasts at the proton torpedoes. The torpedoes detonate, destroying the frontal legs of one of the AT-AT walkers, causing it to topple. The battle droids then flee aboard two Neimoidian escort shuttles, with the rebels following suit. One of the battle droids is accidentally knocked off the ramp of a shuttle. Rex attempts to warn the first of the droid's shuttles to veer to the right. However, the shuttle is shot down by a second AT-AT walker. The remaining droids' shuttle and the rebels' shuttle manage to evade stormtrooper fire.

Having escaped into space, the rebels contact Kalani via hologram. When Ezra asserts that their escape was a victory, Kalani responds that it was a successful strategy but not a victory. Rex supports Ezra and thanks the boy for ending the Clone Wars, an accomplishment that eluded an entire "galaxy of senators." Rex also commends Ezra for discovering a middle ground that entire armies of Clone troopers and battle droids failed to find. Ezra responds that all he did was point out that none of them could prevail in the Clone Wars. Rex and Kalani accept Ezra's explanation and reconcile.
Based on this battle, Kalani calculates that the rebellion has a 1% chance of success against the Empire and concludes that this is where they must part ways. Ezra acknowledges this and salutes him. Rex promises to recount the Battle of Geonosis to Ezra while the two ships separate. At that moment, they are contacted by Hera, who inquires over the intercom about the progress of their mission. Rex informs Hera that they did not manage to acquire the proton bombs but instead found the Ghost a new transport to replace the Phantom.

For this episode, the series logo was redesigned to emulate the style of The Clone Wars TV series, and the Clone Wars theme was played during the closing scene.