In the year 21 BBY, which marks the second year of the Clone Wars, a Galactic Republic squad, under the leadership of Jedi Master Kit Fisto and his former apprentice, Nahdar Vebb, embarked on a mission: to recapture Nute Gunray, the escaped Viceroy of the Trade Federation, who was located on Vassek 3. Upon arriving at the moon, the team followed the signal originating from the Republic cruiser that the Viceroy had used for his escape. This led them to a mysterious fortress situated on the third moon of Vassek. After entering, they thought they had trapped the viceroy, but after defeating five B1-series battle droids, they realized it was just a hologram.
Following this discovery, Count Dooku communicated with the group via hologram, presenting them with an alternative prize. The Jedi and Clone troopers proceeded deeper into the fortress, and after passing several statues, they found themselves in the lair of General Grievous. Dooku had orchestrated the Jedi's arrival on the moon as a test to evaluate Grievous's combat abilities. The Jedi caught the general off guard when he returned to his fortress, and after Grievous killed some of the clones, he managed to escape.
Grievous briefly consulted with his doctor, EV-A4-D, who was preparing to repair him. Meanwhile, Grievous plotted the demise of the remaining clones, with the Jedi narrowly avoiding death each time. Grievous then spoke with Dooku, finding out that the Count had sent the Jedi to test him. Grievous ended his conversation with Dooku by deactivating his hologram. He then engaged Nahdar in lightsaber combat and killed the young Jedi Knight. He subsequently battled Fisto, until the Jedi managed to escape aboard his Delta-7B Aethersprite-class light interceptor, which was piloted by R6-H5.
Grievous provided a report to Dooku, who commented that there was "still room for improvement." Fisto later discussed the mission with Grand Master Yoda and Mace Windu, revealing that Nahdar had tried to match Grievous's power with his own. Yoda stated that this was not the Jedi way and that the war could cause the Jedi to stray from their path.
During the period of the Clone Wars, the planet of Rodia started experiencing shortages of both food and essential supplies. To assist the Galactic Republic in their negotiations with Rodia, Senator Padmé Amidala, a longtime friend of Rodia's senator, Onaconda Farr, was sent to the planet. She was accompanied by her protocol droid C-3PO and Junior Representative Jar Jar Binks. However, when Amidala got there, she found out that Farr had chosen to ally himself with the Confederacy of Independent Systems to get quicker aid for his people. He revealed that Viceroy Nute Gunray from the Trade Federation had promised them both protection and the assistance they needed. Amidala tried to reason with Farr, but she was captured by B1-series battle droids and was scheduled to be executed by Gunray. Simultaneously, Binks discovered a Jedi robe in a closet on Amidala's ship, leading Gunray and his battle droids to mistake him for a Jedi. C-3PO was going to be dismantled, but he escaped and managed to inform Republic Clone troopers about the situation. Binks and Amidala fought against Gunray's forces, and they were eventually reinforced by clones from the 41st Elite Corps, who took Gunray into custody. Soon after, Supreme Chancellor Sheev Palpatine contacted Amidala and Farr, informing them that Republic aid was on its way to help them.
Following the arrival of the Grand Army of the Republic's 41st Elite Corps on Rodia with the Venator-class Star Destroyer Tranquility, under the command of Jedi Master Luminara Unduli and Padawan Ahsoka Tano, the Viceroy was brought aboard the starship. He was placed under high security, guarded by both the 41st Elite Corps and Senate Commandos, an elite division of the Senate Guard, protecting the ship from Separatist attackers, while making voyage to the Republic capital of Coruscant where he would be tried for his crimes against the Republic once again. However, unbeknownst to the Jedi or the viceroy, Dark Lord of the Sith Darth Sidious—publicly known as Chancellor Palpatine of the Republic—and his apprentice Count Dooku—secretly the Sith Lord Darth Tyranus—were already discussing the matter, Sidious knowing that with the viceroy in Republic custody, he would not last very long and eventually reveal secrets, becoming a great threat to their plan. Dooku explained that he had already put a plan into motion to free or silence Gunray, sending his assassin Asajj Ventress to the Tranquility to retrieve him alongside Republic traitor Captain Faro Argyus. Sidious felt uneasy about Ventress being sent on the rescue mission, reminding his apprentice of her past failures that have caused the Confederacy and the Sith numerous losses.
Ventress, along with a battalion of B2-series super battle droids, launched an assault on the Tranquility, boarding the ship using Droch-class boarding ships. The super battle droids engaged the clones in the hangar, while Ventress waited for them to finish off the clones, where she then made her way to the engine room with several detonators in hand, magnetically sticking them across the entire room to cause damage to the ship and create a diversion for Unduli to leave her post to face the assassin. Tano questioned Captain Argyus whether or not she should help her fellow Jedi, knowing that Ventress was too powerful for a single Jedi. Giving the young Jedi advice, Tano chose to leave her post to aid Unduli, allowing Argyus to defeat Clone Commander CC-1004 "Gree" and release the viceroy, where the two made their escape aboard a stolen Consular-class cruiser.
Due to his fleet being near Gunary's position, Jedi Master Kit Fisto was assigned the task of recapturing Viceroy Gunray, who was tracked to the Vassek system's third moon. He was joined by his former apprentice, Nahdar Vebb, who had recently been promoted to the rank of Jedi Knight. Fisto touched down on the rocky moon's surface, where he found Vebb and a squad of clone troopers waiting to begin the search for the viceroy. After discovering the secret panel that opened the massive door, the group went inside the mysterious fortress, making their way through the fortress searching for their target, and they soon managed to find a large room where the viceroy was hiding in, sitting in a chair facing away from the Jedi and clones in the center of the room, guarded by five B1-series battle droids, all of which were quickly destroyed. Using the Force, Nahdar turned the chair around, only to find that Gunray was a hologram, taunting them as he had already left the moon before their arrival. Suddenly, Count Dooku appeared on the hologram and explained that the viceroy was currently safe elsewhere, offering the Jedi an alternative prize, with Dooku suddenly disappearing and one of the buttons on the arm of the chair lit up, with the Jedi pressing it, giving them access to another room.
The entire group went into the newly accessible room and moved past several statues of a strange warrior, soon realizing that they were inside the personal and secret lair of the infamous General Grievous. Unbeknownst to the Jedi and clones, Grievous was approaching his fortress, who was contacted by Dooku about his disappointment with the cyborg general on the "stalemate" in the Clone Wars, believing his best general to having lost his focus on killing more Jedi and claiming more victories over the Republic for Lord Sidious. Meanwhile, inside the fortress, the Jedi and clones found several Jedi braids and lightsabers, deducing them all to be his collection of trophies he's claimed from all the Jedi he has defeated and killed. The clones positioned outside discovered that Grievous was spotted and was heading in their direction, allowing the team inside to hide from the general and ambush him upon entry.
Master Fisto ordered Grievous to surrender upon entering his fortress, stating that if he cooperated, the Senate might show mercy in his punishment. However, the cyborg general immediately drew two lightsabers, activating them both and replying that they would be the ones receiving no mercy for their death, with the battle instantly beginning. Outnumbering Grievous, the clones attached cables to the cyborg and pulled backwards to keep him unsteady for Fisto to land an attack on him, though Fisto removed his the lower half of his legs to cease his movement on legs. Grievous then grabbed onto the ceiling and fought back against the clones, but was brought to the ground, though he persisted and kept moving forward even with the clones pulling him back. Nahdar took the chance to kill Grievous and failed to do so because of his attempt being blocked by Grievous' lightsaber, spinning his hand to throw his lightsaber at Fisto, who knocked it to the ground with his own. Leaping to the ceiling once again, Grievous grabbed one of the clones and used him to attack Fisto, and proceeded to throw the clone at Vebb, knocking him to the ground. Retreating down the hallway, the cyborg managed to get hit by a blaster bolt in his face plate, but soon killed two clones, giving him time to make his escape to his secret control room. Confused by where their target escaped to, Vebb stated that the troops prevented him from defeating Grievous, disappointing his old master.
Upon returning to his castle, Grievous contacted Dooku and informed him that the Jedi had been defeated, but Fisto had managed to escape. Dooku congratulated Grievous on his victory over the clones and the young Jedi, Vebb, but stated that he could have performed better and that there was still room for improvement before leaving the cyborg to contemplate his failures. Despite nearly surviving, Grievous understood the cost of failing the Sith once more. Grievous's hatred for Dooku became stronger as he sensed treachery; it was a betrayal he was unwilling to forgive. However, he would soon have his revenge. Immediately, Grievous ordered that EV-A4-D be recovered and rebuilt to continue to serve him until the conclusion of the war. Realizing he was no longer safe in his fortress, with the Republic having discovered the location, Grievous was forced to abandon Vassek 3 and relocated his base of operations.