Star Wars: The Clone Wars' Citadel arc focuses on the Republic’s efforts to save Jedi Master Even Piell. Piell and his crew have been captured by the Separatist Army because they carry vital information: the coordinates for the Nexus Route, a hyperspace lane that could make travel even more effective and provide a crucial advantage for the Republic in the war. However, despite the great lengths taken to protect the information, their efforts ultimately are futile because Sheev Palpatine is pulling the strings on both sides.
In "The Citadel," the arc's opening episode, the Jedi quickly explain the Nexus Route's importance. While Obi-Wan Kenobi explains how Republic Army could use the Route to gain access to remote Separatist worlds, Anakin Skywalker counters that they could provide similar advantages to the Separatist Army if the Jedi do not recover the information. Other Star Wars media, such as the Star Wars: The High Republic subseries, has since shown how dangerous hyperspace knowledge can be in the wrong hands, and the Jedi fear similar repercussions if the Separatists gain access to the Nexus Route.
The rescue mission is particularly dangerous because Piell and his crew are being held at the Citadel, a seemingly impenetrable fortress built specifically to keep rogue Jedi contained. To even get on to the planet, the organic members of the rescue team must freeze themselves in carbonite to evade detection, a plan devised by Anakin in a nod to his later use of carbonite freezing in Star Wars: The Empire Strikes Back. The Jedi Order's map of the Citadel also is outdated, which forces the rescue team to abandon their initial plans and improvise throughout the rescue. Between the Citadel's defenses and the dangerous terrain of the planet, many of the Clone Troopers are killed, or, unbeknownst to the Republic, taken hostage by the Separatist army.
In the face of these dangers, Piell goes to great lengths to protect the coordinates of the Nexus Route. He destroys the files after memorizing half of the information, while, in his first appearance in The Clone Wars, Captain Wilhuff Tarkin memorizes the other half. Throughout the arc, Piell and Tarkin must travel in separate groups to ensure that even if one group is captured, the information they carry is useless. This strategy makes the escape even harder because, as Tarkin points out, their forces would be stronger traveling together.
Despite all of the team's efforts, Piell doesn't make it out alive. Fortunately, he shares his half of the coordinates with Ahsoka Tano in order to give the Republic a fighting chance. The team does finally escape the planet, albeit with a much smaller group than hoped, and at the end of the arc, it seems as if the Republic has finally gained a true advantage in the war.
Unfortunately, all of these efforts are in vain. While Piell ordered Ahsoka to only share her half of the coordinates with the Jedi Council, Tarkin has made a similar promise to Chancellor Palpatine. Even though Yoda states that he will discuss the matter with Palpatine, Tarkin makes it pretty clear that he will not budge. At the beginning of the arc, Jedi Master Plo Koon notes that these plans could "tip the scale of the war to whomever is in possession of them." But since Palpatine wants the war to continue until he has fully solidified power, he will make sure that both sides have the information. In that way, the Citadel arc shows the true futility of the Clone Wars, because as long as the Republic is unaware of Palpatine’s duplicity, everything it does will be for naught.