"Malevolence Rising" constitutes the second installment of Star Wars: The Clone Wars's first season. Functioning as the series' second episode overall, it initiates a narrative arc spanning three parts. Its original broadcast occurred on Cartoon Network on October 3, 2008, succeeding the debut episode, "Ambush."
A terrifying Separatist weapon creates widespread fear, threatening the Republic's clone forces. Anakin and Ahsoka are in a race against time to save Jedi Master Plo Koon and his clone troopers. After a Separatist warship named the Malevolence attacks, Jedi Master Plo Koon and his team are barely alive. Will Anakin and Ahsoka be able to find them in time?
Jedi Master Plo Koon and Clone Commander Wolffe, aboard the Triumphant, have located the Malevolence in the Abregado system. This Subjugator-class heavy cruiser is under the command of General Grievous and Separatist leaders Count Dooku. They maneuver their fleet of three Venator-class Star Destroyers to engage. Plo advises reporting their location to Anakin Skywalker and Ahsoka Tano, stationed in the nearby Bith system, before the attack. He reveals the location of the Separatist's secret weapon and requests reinforcements. Anakin says he must first consult the Jedi High Council, as he is under orders to protect the staging area. Their communication is abruptly cut off as the Malevolence disrupts the Triumphant's transmissions.
The secret weapon, the Malevolence's powerful ion cannon, fires, disabling Jedi cruisers and making them vulnerable to Grievous' turbolasers fire. Plo Koon, with clone troopers Sinker, Boost, and Commander Wolffe, escape in an escape pod just before their cruiser's destruction. Dooku orders Grievous to deploy pod hunters to eliminate survivors and keep the Malevolence's existence a secret.
Simultaneously, Anakin and Ahsoka participate in a holographic conference with Chancellor Palpatine, and Masters Obi-Wan Kenobi, Mace Windu, and Yoda. Anakin reports the loss of communication with Plo Koon and the likelihood of his fleet's destruction. He suggests a rescue mission, but Master Windu states that all battle groups, including Anakin's, are reassigned to protect supply convoys, leaving no ships available. Ahsoka objects, believing survivors are possible. Anakin apologizes for his padawan's outburst, promises to follow orders, and ends the call. Anakin reprimands Ahsoka for her insubordination, then informs Admiral Yularen that he and Ahsoka will use the Twilight to scout ahead for enemy activity.
Aboard the escape pod, Commander Wolffe reports that the pod's power grid is offline, leaving them adrift without engine, communications, or life support. Koon urges them to restore power for a potential rescue. While repairing, Plo and the clones find another pod. They realize it has been breached and the clones inside are dead, indicating they are not alone.
Emerging from hyperspace, Anakin directs R2-D2 to scan for life. Ahsoka notices they've arrived in the Abregado system and questions Anakin about defying the council's orders, since she was just scolded for doing the same. Anakin explains his intention to rescue any survivors, emphasizing that how they follow orders is their choice.
Continuing repairs, the clones restore communications. They receive a distress signal from a nearby pod and witness a pod hunter attack, breach, and kill the clones inside.
As Anakin and Ahsoka search the debris field, Ahsoka explains her strong feelings about finding Master Koon; he is one of her oldest friends, and he brought her to the Jedi Temple on Coruscant to begin her Jedi training. R2-D2 alerts them to an incoming transmission. Master Kenobi, informed by Yularen of Anakin and Ahsoka's absence, demands answers. He urges Anakin to rejoin the convoy escort to avoid missing the rendezvous with the fleet. Anakin assures him they are en route and ends the transmission. R2 then detects something on the emergency channel.
The pod hunter crew spots Koon's escape pod. They latch onto it. Plo orders Wolffe to maintain the communications signal while he, Sinker, and Boost engage the enemy. The trio defeats the droid crew and destroys the pod hunter, but the loss of contact alerts Grievous to Republic survivors.
Guided by the Force, Ahsoka senses Master Koon's presence and pilots the Twilight to his location. Using the Twilight's tow cable, Anakin and Ahsoka pull Koon's escape pod aboard. A 2-1B surgical droid assesses the clones, stabilizes them, and recommends a medical frigate for full recovery.
The Twilight's sensors detect the Malevolence's approach. Koon, Anakin, and Ahsoka shut down the Twilight's systems, including R2, to avoid detection. They watch as the Malevolence arrives and seemingly passes by. However, the Malevolence detects a faint signal from the medical droid and moves into attack position.
The Twilight powers up and flees. The Malevolence fires its ion cannon. The Twilight navigates the debris field, staying ahead of the energy surge, and escapes to hyperspace. Grievous tells Count Dooku that the Republic will now learn of the ion cannon. Annoyed, Dooku says he will discuss this with his master.
Back aboard Anakin's fleet, Commander Wolffe thanks Anakin for saving them. Anakin praises Ahsoka's persistence. With Master Koon and R2-D2, they leave to inform the Jedi Council about the secret weapon.
The scene with the Malevolence's dialogue and firing sequence is similar to the first Death Star in Star Wars: Episode IV A New Hope.
The second escape pod, Pod 1977, is named after the release year of the original Star Wars.
Boost and Sinker's attempt to restart the escape pod's power grid uses dialogue directly from The Empire Strikes Back when Han Solo and Chewbacca try to fix the Millennium Falcon.