- "Anakin Skywalker has discovered the terrible secret beneath Nelvaan -- a Confederacy laboratory that is transforming the noble Nelvaanian warriors into hideous monsters. On Coruscant, the Jedi try to secure Chancellor Palpatine in the deepest of protected bunkers, but is anywhere safe from General Grievous?"
"This final installment of Star Wars: Clone Wars Volume II takes viewers right to the start of Star Wars: Episode III Revenge of the Sith."
- ―StarWars.com summary
"Chapter 25" is the twenty-fifth and final episode of the Star Wars: Clone Wars animated television series, and the fifth and final episode in Season Three and Volume Two, leading directly into the events of Star Wars: Episode III Revenge of the Sith. The episode originally aired on Cartoon Network on March 25, 2005.
Yoda and Mace Windu continue to cut a swath through the invading droid army on Coruscant. They begin to wonder why such a massive invasion has not attempted to attack the Jedi Temple or the Galactic Senate, and realize that the invasion is a distraction from the Confederacy's real target—Palpatine. Windu jumps aboard an overflying Republic gunship, and orders the pilot to turn around.
Palpatine and his three Jedi protectors reach a hover capsule in a tunnel, and Shaak Ti orders the others to get to the bunker while she holds off their pursuers. She ignites her lightsaber as a group of MagnaGuards troop out of the darkness.
On Nelvaan, Anakin Skywalker tries to fight off the Nelvaan mutants without hurting them. The latest subject manages to burst free of his restraints, smashes the tank and rips the cybernetic chestplates off two of the Nelvaanians. Skywalker soon gets the idea and cuts the rest off using his lightsaber. The half-mutated Nelvaan points to a crystal in the middle of the energy chamber which is causing the damage to the planet.
As Shaak Ti fights the MagnaGuards, she is deprived of her lightsaber and nearly overwhelmed. But she manages to turn the tables by obtaining an electrostaff and destroy several of them with her new weapon. She then manages to reclaim her lightsaber and masterfully wields it in conjunction with the electrostaff.
The Nelvaan warriors are rampaging through the facility, tearing battle droids apart with their bare hands, and freeing their comrades from captivity. Skywalker leaps to the top of the generator, then lowers himself into the crystal chamber. Screaming in agony, he reaches his prosthetic arm into the energy sphere, uses the Force to pull the crystal from its socket, and then shatters it into a thousand shards. The energy surge causes the generator to explode, and Skywalker leaps to safety, his arm destroyed. The Nelvaan warriors reach the planet's surface, where the waiting battle droids are destroyed as the planet's ice age comes to an end. An enraged Skywalker clambers to the surface, where he kills the Techno Union scientists trying to flee in their ship. Seeing Skywalker's ravaged arm, the Nelvaan mutants worship him as "holt kezed"—"ghost hand"—their savior, and in solidarity they tear the implanted weapons from their own arms. Skywalker and the Nelvaanians return to the village. The women are at first horrified by the mutants, but when a child recognizes her father, the familial bonds are restored.
On Coruscant, Foul Moudama and Roron Corobb manage to get Palpatine into his secure bunker. Once they are locked inside, they discover that General Grievous has beaten them to it, and the two Jedi leap forward to defend their leader, who sinks, seemingly unconcerned by the danger, into the shadows. As Moudama and Corobb manage to get Grievous in a saber-lock, his arms split along their lengths into four. His extra two arms then grab the remaining two lightsabers on his waist, and Grievous lunges forward.
Shaak Ti continues to fight off Grievous's MagnaGuards, but when the droids suddenly retreat, she realizes they've been keeping her busy while Grievous reaches the others. As she races to the bunker, Grievous finishes off the other two Jedi, before turning to and threatening Palpatine. Palpatine calmly replies that Grievous wouldn't dare hurt him, for fear of his master's wrath. Grievous venomously replies that Palpatine is lucky he's wanted alive.
Just then, Shaak Ti arrives. Horrified to see the bodies of her comrades, she charges Grievous. Grievous easily grabs the exhausted Jedi by the throat, relieves her of her lightsaber, and activates snaking cables from his wrist, announcing he has other plans for her.
The droids on Grievous's ship open fire on the gunship with Mace Windu on board. As the vessel falls from the sky, Windu jumps to safety. Grievous turns to face him, igniting four lightsabers, but Windu uses the Force to crush the chest plates protecting the General's organs. Grievous turns and flees on board, coughing furiously. Windu tries to leap after the ascending ship, but the vessel's blaster barrage forces him to defend himself, thus robbing him of the power behind the leap, and the ship blasts into space. He rushes into the bunker to find the two dead Jedi, with Shaak Ti trussed and tied to the ceiling, devastated by her failure to protect the Chancellor.
R2-D2 is helping Skywalker repair his arm, when an urgent message is received from Mace Windu on Coruscant.
- "Kenobi, Skywalker, Coruscant is under siege, and General Grievous has abducted the Supreme Chancellor. You must return immediately! You must rescue Palpatine!"
- ―Mace Windu announces that Palpatine has been kidnapped
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