Returning from a dangerous assignment, Jedi Master Even Piell's cruiser had fallen under Separatist attack. Seeking the crucial intel he carries about the secret Nexus Route hyperspace lane, which can provide a strike force with easy access to key worlds on both sides, the Separatists captured him and his crew alive, and transferred them to a prison designed to hold Jedi: The Citadel. Obi-Wan and Anakin are tasked to lead a team of Clone Troopers to rescue Piell and his men, with Ahsoka Tano sneaking aboard their ship to take part in the mission.
- Air-Vent Passageway: Subverted and lampshaded by Ahsoka. With the entry point the Jedi wanted to use blocked, Anakin and Obi-Wan debate how to get in, and Ahsoka points out the ventilation hatch. Anakin brushes this idea off it had already come up in planning and been dismissed because no one on the team is small enough to squeeze through the vent but Ahsoka, who stowed away to join the mission, is small enough to make it, barely.
- The Alcatraz: The eponymous Citadel, which can be found on a remote, volcanic half-of-a-planet. The tower is full of traps, and guarded by battalions of Separatist droids. It's explicitly stated that even if someone manages to escape the building, they still can't really go anywhere because the broken, lava-strewn landscape is almost impossible to cross especially while being chased. And then to get off the planet they need a ship, and then make it past the Separatist blockade.
- Ascended Extra: Even Piell, who had no spoken lines in the two Prequel Trilogy films he appeared in, receives a fleshed out expanded role in this episode (along with the storyline it is part of). Captain Tarkin might also count.
- Blatant Lies: When Ahsoka is released from the carbonite with the rest of the team, despite Anakin forbidding her from joining the mission, she tries to excuse herself with a not quite well-thought-out lie:Ahsoka: I received orders to join the team. I thought you knew.
Anakin: Orders? From who?
Ahsoka: I discussed it with Master Plo.
Anakin: He didn't tell me.
Ahsoka: You were already in carbonite.
- Anakin's uncharacteristic overprotectiveness towards Ahsoka isn't all that surprising once you remember what happened to her in "Altar of Mortis", which is two episodes earlier.
- After Echo got new Phase II armour for being promoted to ARC trooper, he painted Rex's handprint on it, which Rex put on his original, "shiny" armor using a Rishi eel's blood, way back in "Rookies". Similarly, Fives has painted a stylized Rishi eel on his own helmet, as a reminder of their teammate Cutup, who was eaten by one of the eels.
- Anakin's idea to bypass the lifeform scanners is to carbon-freeze the entire infiltrator team. Fives' reaction takes it home:Fives: [examining the carbon freezer] Are we sure this thing is safe? I don't wanna end up a wall decoration.
- The Nexus Route is a secret hyperspace lane that the Separatists could potentially use to surprise-attack Coruscant.
- Anakin's idea to bypass the lifeform scanners is to carbon-freeze the entire infiltrator team. Fives' reaction takes it home:
- The Cameo: C-3PO appears briefly, incredulous that R2-D2 has a squad of reprogrammed battle droids to command.
- Climbing the Cliffs of Insanity: The strike team has to climb a vertical cliff in order to reach an entrance to the prison. With their hands, since they can't use grappling lines because of electro-mines.
- Complaining About Rescues They Don't Like: Tarkin is not happy with his rescuers' tactical decisions, because he isn't a big fan of how the Jedi are conducting the war in general.
- Double Take: Anakin, on seeing Ahsoka when the strike team is released from carbonite.
- Electric Torture:
- The interrogator droid first tries this to get the intel from Master Piell.
- Osi Sobeck electrocutes Anakin while he is captured by an electromagnet stuck to his mechanical arm.
- Eye Scream: Master Piell had already lost his left eye prior to The Phantom Menace, and after the Electric Torture fails, the droid attempts to gouge out his other with a needle in its hand. It's millimetres away from doing so when the rescue team arrives.
- Family-Unfriendly Death: One clone falls while scaling a cliff, and detonates an electro-mine. Another is killed by an electrified wall trap.
- From Nobody to Nightmare: Tarkin is still just a simple Navy Captain here. Flash forward 20 years, and he's the commander of the Death Star, and destroyer of Alderaan.
- Human Popsicle: Anakin freezes the entire infiltration team in carbonite and uses droid pilots to evade the Citadel's life-form scanners.
- Let's Split Up, Gang: Obi-Wan suggests splitting into two groups, so that even if one party is captured, the enemy would only have half of the intel, while Tarkin counters that a stronger, unified team has a better chance of protecting it. Ultimately Piell decides to go with Obi-Wan's plan.
- MacGuffin: The Nexus Route coordinates are known by Captain Tarkin and Even Piell, forcing the Jedi and the 501st to recover them no matter the cost.
- Oh, Crap!: The warden Osi Sobeck has one upon realizing that the Jedi have managed to infiltrate the Citadel.
- Shattered World: Some past cataclysm has pulverized half of the planet Lola Sayu, with the still-glowing mantle exposed to space and the remaining crust forming an Asteroid Thicket around the world. The Citadel itself is built near the exposed zone so that any escapees must face a Lethal Lava Land with very few possible landing sites for hostile ships.