On the planet Christophsis, a relief effort by Republic senator Bail Organa has been trapped by a Separatist blockade. A task force led by Anakin Skywalker attempting to rescue the Senator's forces has been halted by the spider-like Admiral Trench. Anakin is about to order a suicidal charge past the Separatist line when another Venator-class Star Destroyer commanded by Obi-Wan Kenobi arrives from hyperspace. Noting that Anakin disobeyed his order not to engage the enemy until he returned, Obi-Wan calls on Anakin to pull back, as he has a new weapon to use.
Anakin takes a shuttle to Obi-Wan's ship and is shown a IPV-2C Stealth Corvette, which is a prototype stealth ship. Obi-Wan wants Anakin to use the stealth ship to slip past the blockade and deliver badly-needed supplies to Senator Organa. As Anakin prepares to move out, Admiral Yularen recognizes the signature symbol and tactics of Admiral Trench, whom he thought killed in the Battle of Malastare Narrows years before the Clone Wars. He contacts Anakin and warns him about who he's up against, volunteering to accompany Anakin on the mission and advise him.
As the mission gets underway, rookie clone trooper CT-1284, nicknamed Spark, also boards. The stealth ship launches and cloaks to clip past the Separatist fleet. The stealth ship's cloak works perfectly, allowing the ship to pass within spitting distance of a frigate undetected.
Back on the Separatist flagship, Trench and his tactical droid are assessing the situation. Trench decides to pressure the Republic by bombing Organa's position in order to draw the Republic fleet out. Unfortunately, the bombers are about to fly right through Anakin's airspace. Unable to attack without dropping their cloak, Anakin tensely chooses not to engage as the droid bombers fly past without incident. As they strike, Organa desperately calls Obi-Wan for help. Yularen and Anakin advise against Obi-Wan attacking, and Anakin decides to try for a decapitation strike on Trench himself.
Trench begins to suspect something when Obi-Wan fails to rise to the bait. Anakin decloaks and fires torpedoes at Trench's bridge, but they impact harmlessly on his shields. Trench fires back with his own missiles, but Anakin fires flares and recloaks, changing his vector under cover of invisibility. In response, Trench fills the area with turbolaser fire, to no effect. Trench realizes that a Jedi must be piloting the ship.
Admiral Trench sends out a message on all open channels, commending Anakin's bravery in challenging him, but cautions that he has faced and beaten ships armed with cloaking devices before in addition to saying that his attack has failed and Christophsis will fall to the Confederacy. Trench recognizes that the Jedi in command of the cloaking ship is more likely to attack him again rather than try to slip past the blockade.
On board the stealth ship, Anakin, Yularen, and Obi-Wan confer that Trench has fought cloaked vessels before and use tracking torpedoes to hit them. Obi-Wan and Anakin note that most ships with cloaking devices are much larger than Anakin's little ship. Anakin figures that Trench is homing in on the ships' magnetic signatures.
Anakin decloaks and fires on Trench again. Trench orders to lock on and fire the tracking torpedoes, but has to lower his shields first. The torpedoes lock on, but Anakin diverts all power to the ship's engines and heads straight for Trench's command ship, leading the missiles straight back to him. With his shields unable to recharge in time, Trench resigns himself as his ship is once again blown up.
With Trench's flagship destroyed, Obi-Wan and Commander Cody launch a new attack on the leaderless Separatist fleet, while Anakin and Yularen pilot the stealth ship down to Christophsis to deliver the vital supplies to Organa and his men. Senator Organa gives his gratitude to Skywalker, and Yularen expresses both concern and admiration for Skywalker's daring, if unorthodox, tactics.
- Anachronic Order: This episode, despite being the sixteenth episode in the series' second season, is chronologically the first episode of The Clone Wars and takes place before "The Hidden Enemy" (1:16) and the pilot movie.
- Character Tic: Admiral Trench tends to click his mandibles together after every few sentences.
- Deadly Dodging: Anakin uses this tactic to defeat Trench by leading the tracking torpedoes back to Trench's flagship while its shields are still recharging.
- Diverting Power: After getting Trench to take the bait and drop shields to launch magnetically locked torpedoes, Anakin drops all cloaking on his stealth ship to dedicate that power to the engines.
- The Dreaded: Trench is this trope as a result of his status as an effective Separatist admiral. Admiral Yularen is visibly unnerved upon recognizing Trench's symbol on his flagship.
- Expy: Let's see here, Admiral Trench is a methodical commander working for the enemy who is a brilliant tactician and well-versed in handling cloaked ships. Are you sure this isn't Grand Admiral Thrawn?
- Face Death with Dignity: When Trench realizes that he has been defeated by Anakin, he doesn't scream or shout, merely facing the incoming missiles about to destroy the bridge quietly as he closes his eyes.
- Freeze-Frame Bonus: After a supply ship gets hit, there's a shot of a screen on the bridge of the Resolute showing an "Enemy Ship Profile". Translating the Aurebesh reveals that the text comes from the Wookieepedia article on the Sith Dreadnaught cruiser (complete with a  notation and an anachronistic use of "BBY").
- Mauve Shirt: Blackout and Spark.
- New Meat: Spark is this. He is officially welcomed as a proper member of the crew towards the end of this episode.
- Oh, Crap!: This is Yularen's reaction when he recognizes Trench's symbol.
- Poor, Predictable Rock: Admiral Trench insists on using the same tactics as have worked for him against cloaked ships in the past, ignoring that his opponents know about those battles.
- Spiders Are Scary: Trench is a Harch (a giant tarantula-like alien species), and he is definitely full of menace.
- Stealth in Space: Although cloaking devices have been mentioned before in Star Wars, this episode is the first time they are shown onscreen in the canon. This episode shows that they are not perfect and can be detected if you know how to look.