High above the overgrown fungal world of Felucia, a trio of Republic cruisers pound a blockade of Separatist frigates. From the starboard hangar of one of the cruisers emerges a stream of attack gunships escorted by V-19 Torrent interceptors. Leading the reinforcements is Jedi Master Plo Koon, aboard the blue-decorated Jedi starfighter gifted to him by Anakin Skywalker during the Malevolence crisis. He calls to his clone wingman, Warthog, to protect the gunships as he takes out the droid fighters. The gunships run through the blockade, with only a pair of vulture droids surviving to give pursuit.
The gunships penetrate the atmosphere, vectoring toward a landing zone clear of the immense pitcher plants and other exotic flora of Felucia. On the ground, a small clone fighting force is surrounded by battle droids that tighten the circle around them. Obi-Wan and Anakin block incoming fire, standing beneath a mighty AT-TE walker.
In the air, Warthog desperately evades to no avail as the droid fighters pursue. Plo Koon swings his vessel around, blasting apart one of the vultures. The other droid gets caught in the explosion and spins out of control, smashing the ground hard and tumbling into an AT-TE. The Jedi dodge the collision, and realize that reinforcements must be on their way.
Cody and Rex lead their beleaguered ground forces to the landing rescue gunships. Anakin and Obi-Wan radio Ahsoka, who should be returning from her assigned patrol duty. She's in the thick of battle as well, deflecting incoming laser fire while standing atop an immense clone turbo tank. She's six kilometers east of the Jedi Knights, and her forces have engaged the enemy. Kenobi orders her to prepare for extraction, but she refuses to retreat. Kenobi restates his order, but Ahsoka instead follows Skywalker's maxim of never giving up when the enemy is on the run.
The Republic gunships approach Ahsoka's troops. She continues to advance, forcing Anakin to land the evacuation craft directly in her path, thus causing her to stop. Anakin jumps out of the gunship and orders Ahsoka aboard. He tells her that the droids are about to overrun her postion, but she cannot see it from her vantage point. Reluctantly, Ahsoka boards the gunship, and as it lifts off, she does indeed see that dozens of droid reinforcements stood ready to ambush her if she had continued her push forward.
Later, on Coruscant, within one of the spires of the Jedi Temple, Ahsoka is being debriefed by the stern Jedi Council. Ahsoka admits her error, citing being caught up by her apparent successes to not see the battle as a whole. Anakin takes responsibility for Ahsoka's failure; he attributes her advanced abilities for his oversight of her youthful shortcomings. Nonetheless, Mace pulls Ahsoka from battlefield duties, and Yoda assigns her to guard duty at the Jedi Archives.
Deep inside the Jedi Archives, Ahsoka meets Jocasta Nu, the director of this vast information depository. Madame Jocasta gives young Ahsoka a tour. The Jedi Temple library contains more knowledge than anywhere else in the galaxy, and is even said to contain forbidden knowledge that only the most learned of Jedi Masters could access. The deepest secrets are contained within the holocron vaults, where holocrons - data storage systems that can only be opened through the Force - reside. Ahsoka is not allowed inside. Even Madame Jocasta has not set foot within the vault for years.
In the Coruscant underworld, within a seedy hotel, Cad Bane stands inside a dingy room, biding his time. A hologram of Darth Sidious appears. Sidious tasks Bane to acquire a Jedi holocron for him. Bane notes it won't be easy - to do so would require him to infiltrate the Jedi Temple. So, it will be a costly assignment. He requests a rogue-starfighter with elite weapons, a cloaking device, and triple his usual rate. Sidious agrees, and will provide Bane with the means to infiltrate the temple.
In the Jedi war room, Anakin and Obi-Wan examine the ramifications of their loss of Felucia. Yoda is distracted by a disturbance in the Force. He senses that the Jedi Temple will be host to danger... intruders are on their way.
In his apartment, Bane hunches over Todo 360, his fidgety techno-service droid, as he implants a small security chip into a slot in the droid's back. The two are joined by Cato Parasitti, a Clawdite changeling. She is part of Bane's plot to steal a holocron. The two pull up intelligence provided by Darth Sidious on Bolla Ropal, a Jedi Knight in the Mid Rim. He's part of the next leg of their assignment. First, though, the two hunters must infiltrate the Temple. The chip that Todo carries is a piece of the puzzle: he has all the technical data regarding Temple security systems. Also provided by Sidious are detailed holographic maps of their destination.
The last element is where Parasitti comes in. Bane's hotel is now the final resting place for the late Jedi Knight, Ord Enisence. Parasitti adopts the form of Enisence, and will serve as Bane's "inside man," entering the archives and monitoring Bane's progress. The two will maintain contact with compact ear-comlinks.
The library's placement near the communication center will provide a challenge - it's an area swarming with Jedi - as will the security systems of the vault, but Bane seems confident of his success.
Back at the Jedi Temple, Anakin and Obi-Wan are on alert and busy hypothesizing what intruders might be after. They incorrectly theorize that the east tower communications center is the likeliest target, as it houses Jedi transmitter codes and crucial war information. Skywalker dashes to the tower, while Kenobi heads to the central security station to monitor perimeter defenses.
Outside, Bane and Todo use rocket boots to flit to an untended overhang amid the Jedi Temple's enormous architecture, near the south tower. Inside, Ord Enisence strolls into the Temple. Ahsoka greets him warmly, but Enisence only returns cold impatience. Ahsoka drops the matter, but Jocasta overhears the unusual outburst.
Parasitti takes a seat at a terminal within the archives, and begins guiding Todo to a weak spot in the defensive shields surrounding the Temple access points. Parasitti also disrupts the local scanners to provide Todo and Bane the cover they need to enter.
Obi-Wan and Anakin notice the glitch in the scanners, but detect no intruders from their respective vantage points. Yoda senses trouble afoot, but is also at a loss as to what the potential target may be. As they begin to speculate about communications center, Obi-Wan runs a scan on the central ventilation shaft, and detects a disruption by the south tower. Kenobi and Skywalker go to investigate while Yoda places the temple on high alert.
Bane and Todo enter the cavernous ventilation systems. Parasitti guides them to the control boards that bypass the massive fans. One set, however, remains active, and nearly sucks the intruders into its cutting blades before Cato deactivates it in the nick of time.
Jocasta confronts "Enisence" with word of the Temple being on high alert. Enisence lashes out and knocks the librarian unconscious. Parasitti then adopts her visage with her shapeshifting skills. Bane and Todo arrive at the vent shaft above the vault, which is protected by a dense laser web. Cato remotely deactivates the laser webs.
Obi-Wan and Anakin arrive at the top of the vent shaft to see where the infiltrators entered, and try to follow their path. They rappel down the enormous tunnels, following the network of shafts to the communications center.
Anakin and Obi-Wan explore the side vents of the central vent shaft, but find no sign of the trespassers. They are too deep inside the Temple for the general sensors to detect. Yoda speculates that they may be receiving assistance from inside the Temple.
Outside the Jedi Archives, Todo and Bane deactivate the last of the laser screens. Bane next has an odd request for Todo: to cut through the wall, but not in the direction of the vault; instead, the droid is to cut his way to the communications center.
In the library, Ahsoka receives a comlink transmission from Yoda, warning of an intruder possibly posing as a Jedi. The Jedi Master tasks the Padawan to find Jocasta Nu. She spies Jocasta making a suspicious transmission. Ahsoka confronts her, but Cato ignites Jocasta's lightsaber and attacks Ahsoka. Untrained with the Jedi weapon, it's all Cato can do to hold off Ahsoka, buying enough time to run for it. Ahsoka uses the Force to send a chair tumbling into Cato's path, tripping up the changeling.
As Anakin and Obi-Wan continue their search, Ahsoka communicates with her Master. She's interrogated Cato and discovered that the intruder's objective is the holocron vault. Kenobi dismisses this, as only a Jedi can activate a holocron. Based on this, Anakin surmises that the intruder must be trying to get to the communications center through the vault.
Meanwhile, at the vault gate, Bane requires Cato's assistance to cut through the last security gate. His comlink transmission is met with silence, however, since Cato's been caught. Shifting gears, Bane dispatches Todo to the communications center. The little droid nervously complies - he knows that it's filled with Jedi. As the droid departs, Cad produces a small device - the same kind of "security chip" he implanted in Todo earlier - and sticks it to the access panel. It counts down to zero and explodes.
The blast shakes the access tunnel that Obi-Wan and Anakin currently occupy. They follow the tremors to the blast site and immediately see Todo's cut path to the communications center. They give pursuit. Bane emerges from the shadows, having successfully misdirected the Jedi. He enters the holocron vault and grabs the appropriate cube.
Meanwhile, in the Jedi communications center, Mace Windu, Aayla Secura, Kit Fisto, and Yoda turn to spot Todo suddenly emerging from an access hatch. Mace Windu detects a bomb within the droid and Force pushes it away. Anakin and Obi-Wan take cover in the vent shafts as Todo suddenly explodes.
Back in the archives, Ahsoka marches a bound Cato and checks in with a revived Jocasta Nu. Bane, meanwhile, sneaks away hidden beneath a Jedi robe. Yoda and the other Jedi Masters examine the holocron vault, and find a cube missing. This whole caper was never about war intelligence. As the Jedi attempt to puzzle their enemy's agenda, Cato offers up some information on Bane's next target: Bolla Ropal.
Ropal is the keeper of the Kyber crystal, a data repository of every known Force-sensitive child in the galaxy that can only be read within a Jedi Holocron. Bolla is in the Devaron system, out of range for a warning. Ahsoka and Anakin decide to go to Devaron to alert him, while Kenobi will see to Parasitti's incarceration as well as look for Bane on Coruscant.
*Recap Thanks to: StarWars.com