"Children of the Force" represents the third installment of Season Two from the Star Wars: The Clone Wars animated television program. As the series' twenty-fifth episode, it brings a three-part narrative arc to its conclusion. Chronologically, it takes place before the events of the seventeenth episode of Season Two, specifically "Bounty Hunters".
After their unsuccessful endeavor to retrieve the holocron stolen by Cad Bane, who they mistakenly believe is deceased, Anakin Skywalker and Ahsoka Tano arrive aboard the Resolute, which is in orbit around the Devaron System. Tano persistently questions the clone trooper Denal, who supposedly eliminated Cad Bane and sustained injuries, but receives no response. Meanwhile, Skywalker discovers a trace of green Duros blood on the floor of the shuttle they used for their return, alerting him to an impending threat. He attempts to warn Tano, but his warning comes too late. Cad Bane, disguised as the clone trooper, delivers a forceful knee strike to her chest before fleeing towards the fighters to escape. Skywalker tries to intercept him by leaping onto the fighter, but Bane maneuvers the ship into the vacuum of space, forcing Skywalker to jump off. Powerless, Skywalker then contacts Admiral Yularen and instructs him to disable the hyperspace transport rings; however, Yularen hesitates by questioning the order, which delays the lockdown, allowing Cad Bane to successfully escape.
Upon their return to Coruscant, Skywalker and Tano inform the Jedi High Council about the unfortunate developments. With Bane now in possession of the holocron's list of Force-sensitive children, this information has fallen into the hands of the Separatists, posing a significant threat to the Order. Their sole recourse is to utilize the Force to monitor for any abduction attempts.
In another location, Darth Sidious directs Bane to abduct four Force-sensitive children and transport them to Mustafar. Bane finds the kidnapping of innocents to be a drastic measure, yet remains indifferent as long as he receives payment.
Yoda, Obi-Wan Kenobi, Mace Windu, and Skywalker engage in meditation, endeavoring to locate any children through the Force, although many are obscured by the dark side. Skywalker then proceeds to Naboo to safeguard a Gungan child, while Kenobi travels to Rodia.
On Rodia, Bane impersonates a Jedi, asserting that he is there to escort the child Wee Dunn to Coruscant. The child's mother objects, citing that Master Bolla Ropal had deemed him too young for such a journey. Bane insists, falsely claiming that there are "impostor" Jedi at large, but Wee's mother refuses to release him. Bane then employs a spinning device to "relax" her.
Shortly after, Kenobi arrives on Rodia, rushing to the Dunn residence. However, Wee's mother threatens Kenobi with a blaster, which he disarms from her grasp, demanding to know Bane's whereabouts. Bane then appears in the doorway, before escaping to his fighter and fleeing.
On Naboo, Skywalker and Tano arrive to protect the Gungan child Roo-Roo Page. Tano is assigned to watch over her in Jan-gwa city. Later that night, Bane infiltrates the Gungan city. He sneaks into Roo-Roo's room, only to discover Tano awaiting him. They engage in a brief skirmish before he is apprehended; Tano reclaims her Padawan braid.
Aboard a Venator-class cruiser, Bane refuses to disclose the location of the other captured children, and the navigation logs of his ship have been erased. Consequently, Skywalker, Windu, and Kenobi attempt to simultaneously employ the Mind Trick to compel Bane to reveal their location, risking the destruction of his mind. The ordeal proves taxing for Bane, and he ultimately cooperates.
With Bane as their guide, Kenobi and Windu prepare to locate the children. Windu mentions that the Chancellor is pressing for a report, but Kenobi retorts that this is a matter for the Jedi; Skywalker suggests contacting Palpatine.
On Coruscant, Skywalker informs Palpatine about the plot. He expresses his conviction that even Count Dooku is not behind it. The Chancellor inquires about Skywalker's suspicions, to which he admits he doesn't know; Palpatine advises him to exercise patience.
On Mustafar, Palpatine, in his guise as Sidious, appears via hologram and instructs the surgical droids to prepare for the children's surgery. He reveals his intention to create an army of Sith spies to overwhelm the Jedi. He dismisses any potential loss of the children during the procedure as inconsequential.
The Jedi shuttle arrives at the station indicated by Bane, but the masters do not sense the children's presence. Bane claims that the children are safe and that he only brought them to the holocron. He offers to retrieve it, but Windu refuses to be deceived, inadvertently triggering the bridge's sensors, activating several turrets. The Jedi defend themselves as Bane departs the station in an escape pod. Fortunately, they secure the holocron and escape the station before it self-destructs.
Back on the Resolute, Skywalker and Tano examine Bane's fighter for any clues. Tano discovers volcanic ash on its hull, while Skywalker reviews its fueling log, deducing that Bane had left his hostages on Mustafar. They then depart in the Twilight. However, their approach is detected, and Sidious orders the children to be relocated and the facility destroyed. The Master-Padawan duo then enter the facility, drawn by Wee's cries. However, the droids use the children as shields while fighting the Jedi, as the facility falls apart. However, the Jedi managed to snatch the children away from the droids and escape before the entire facility collapses into the dangerous lava lake.
Upon their return to Coruscant, Skywalker admits to the Council that they were unable to ascertain who was behind the kidnappings. Yoda urges caution moving forward.
Plans were in place to feature the Gampassa, a massive turtle-like creature inspired by the Hah-nu-nah from Native American oral traditions, but it was ultimately omitted.
The episode's opening scene mirrors the closing scene of "Cargo of Doom," but this time focuses on the clones instead of the Jedi. However, in the earlier version, Cad Bane (disguised as Denal) passed Anakin and Ahsoka as he walked out of the ship. In this episode, they are in a different place and talking to another clone trooper instead of Admiral Yularen.
During the attempt to lock down the hyperdrive rings, Admiral Yularen exclaims, "No, lock them all down! Hurry!" echoing a line spoken by C-3PO when instructing R2-D2 to shut down the Death Star's trash compactors in A New Hope.
On Black Stall Station, Mace Windu slides under a closing door, then reaches back to retrieve his lightsaber using the Force. This action alludes to a recurring comedic element in George Lucas' Indiana Jones film series, where Indiana Jones reaches under a closing door to grab an important item such as his hat or whip.