Aboard a Jedi cruiser, Jedi Knights Anakin Skywalker and Obi-Wan Kenobi examine an intercepted message from General Grievous to Asajj Ventress. The Jedi learn that Kamino will be their next target. The Separatists want to stop the production of new clones if they are to win the war.

Obi-Wan thinks the Separatists are taking quite a chance targeting Kamino. The clones in the briefing room ask to be part of the mission since their home planet will be the next target. Anakin Skywalker tells them to get the troops in the 501st battalion to prepare to travel home to Kamino.

Anakin Skywalker and Obi-Wan Kenobi travel with clone troopers Captain Rex, Commander Cody, Broadside, Echo, and Fives of the 501st to Kamino to warn Shaak Ti and Lama Su of the Separatist attack. Lama Su thinks the Republic blockade is far too strong for the Separatists.

Clone troopers Echo and Fives walk down a hallway full of young clone cadets headed to target practice and remember their youth in the cloning facility. They spot their old friend 99, the maintenance clone who asks after his friend Hevy only to learn that his clone brother died valiantly in battle. Echo and Fives inform 99 that they've returned due to a possible attack on Kamino. 99 offers to help.

General Grievous and his cruisers suddenly arrive, ready for battle. As the Separatist fleet presses their attack on the Republic cruisers, Anakin Skywalker and R2-D2 fly out of the hangar to help defend Tipoca City. Anakin always prefers being in the middle of the action rather than stuck in a command center.

Shaak Ti, Obi-Wan Kenobi, Lama Su and clone commanders watch the battle on their holoscreen in the command center. Shaak is surprised that the Separatist fleet is so small and orders for the air strike to begin.

As debris falls from the space battle above into the ocean on Kamino, Shaak Ti notices that Grievous appears to be sacrificing transports in favor of protecting his command ship. Obi-Wan suspects that something is not right.

Inside Asajj's underwater Trident ship, hidden beneath the waves of Kamino, battle droids notify her that reinforcements have arrived. Asajj orders the battle droids to send out the aqua droids to assemble the assault craft out of the carefully concealed debris dropped into the oceans.

Anakin Skywalker tells the troopers to focus their attack on the Separatist cruisers. Anakin wants to press the attack, but Obi-Wan tells him to wait. This battle is too easy. Not even Grievous would attack so recklessly. Obi-Wan is suspicious of the debris falling from General Grievous' ships and wants to take a closer look.

Obi-Wan travels beneath the Kaminoan waves to investigate the debris. He soon learns that they are actually parts for attack crafts being assembled by aqua droids. The droids notice Obi-Wan and attack his ship. Obi-Wan launches an escape pod with aqua droids still attached.

Obi-Wan Kenobi ejects from the escape pod, making a narrow escape from the aqua droids by riding an aiwha into the air. He calls for backup from Anakin Skywalker.

The completed droid attack craft -- Trident drill ships -- bore through the walls of Tipoca City and unload aqua droids ready for battle. General Grievous arrives with the aqua droids and orders Tipoca City destroyed.

As they fend off fire, Obi-Wan tells Anakin Skywalker that he thinks there are not enough droids for them to capture the entire city and that this attack is just a distraction. He orders Anakin to go and protect the clone DNA chamber while he deals with Grievous.

99 brings Fives and Echo more ammo including grenades. During the battle, young cadets join the clone forces. 99 offers to show them a shortcut.

As General Grievous makes his way through the facility, Asajj Ventress shows off her skills by Force choking and stabbing an unfortunate clone trooper with her lightsaber. Grievous compliments her on her style.

Asajj scoffs at the idea that Grievous thinks they are equals. Grievous reminds her that he is the general in charge of the assault and she is just tagging along to recover the clone DNA. The Separatists hope the DNA might unlock new military possibilities to overcome the Republic.

Back in the barracks, the inexperienced cadets ask the clones and 99 what should do. The troopers tell the children that their training is in the blood, just like any other clone. This is their home, therefore this is their war. 99 offers to help them find the armory.

Shaak Ti, Lama Su and the clone troopers are under attack at the command center. Shaak Ti slices apart the invading aqua droids. With the droids spread thin, Shaak orders the troops to take offensive action.

Asajj has found the clone DNA chamber and secures a DNA sample. Anakin Skywalker catches up with Asajj at the DNA chamber to confront her.

99 leads the cadets and troopers to the armory which holds everything they need to fight the aqua droids. Under attack from battle droids, 99 tosses ammo to the clone troopers as they throw grenades at the droids. While hobbling off to get more grenades, 99 is shot down by a battle droid and dies.

Grievous and Obi-Wan duel with lightsabers on a landing platform which is soon crushed by a Trident unit causing both opponents to fall. While Grievous scurries to safety, Obi-Wan is again saved by the aiwha.

Asajj and Anakin continue their lightsaber duel outside on one of the platforms. Using the Force, Anakin snatches the DNA sample from Asajj, who finds herself quickly outnumbered by several angry clones. She jumps onto Grievous' fleeing escape pod and makes her getaway.

While the young cadets celebrate their victory, the older clone troopers mourn the loss of 99. Echo and Fives stand at attention when Clone Commander Rex and Cody commend them on their actions during battle, and are promoted to ARC troopers.