Count Dooku issued two coordinated orders. General Grievous would take a Separatist fleet to Coruscant and kidnap the Chancellor. At the same time, Asajj Ventress would bomb the Jedi Temple while most Council members were off-world.
Shepard received advance intelligence of the operation. He did not warn the Republic. Instead, he deployed nano-assassin droids with two mission objectives inside the Jedi Temple:
Vault Unit:Infiltrate the restricted vault levels. They carried compact plasma saws to cut open vault doors without explosive signatures. Their task was to remove all artifacts and secure them inside Shepard's newly developed dimensional storage cubes, a technology capable of storing extremely large mass-volume items in stabilized spatial pockets. These cubes were large enough that he had already stored his partially-built mothership framework inside one. For Jedi artifacts, volume was not a limitation.
Archive Unit:Penetrate the Jedi Archives and download all available data, including sealed, erased, and restricted files. They were to extract complete data blocks directly from terminal cores and archive servers into portable storage modules.
When the Separatist fleet dropped out of hyperspace above Coruscant, orbital fighting began. Grievous boarded the Chancellor's secured location and captured him. Republic defenses responded, sending Jedi starfighter escorts toward Grievous' flagship.
During this distraction, Ventress executed her part of the plan. Explosives detonated inside the Jedi Temple, causing structural damage, fires, and panic. The blast created an ideal access window for Shepard's nano-units. With temple security overwhelmed and attention diverted to casualties and fire suppression, the droids proceeded to their targets.
The Vault Unit reached the lower secured levels, cut through thermal seams of the vault doors, and emptied the contents into dimensional cubes. No alarms were triggered due to low-signature thermal cutting.
The Archive Unit entered the data section and began high-speed extraction from network cores. With internal security systems disrupted by the bombing, they bypassed encrypted partitions and copied the full archive dataset, including restricted historical records and sealed directories.
Meanwhile, the Republic response proceeded as in canon: Anakin Skywalker and Obi-Wan Kenobi intercepted Grievous' flagship, boarded it, fought through droid forces, and moved to recover the Chancellor.
As the flagship battle concluded, the Jedi Temple bombing was still being contained. Smoke filled multiple wings, and emergency personnel focused on triage and evacuation. Shepard's nano-units completed extraction and withdrew, leaving no functioning hardware behind.
The result matched Shepard's operational goals:
The Chancellor was kidnapped by the Separatists.
The Jedi Temple was damaged and bombed.
Under the cover of this event, Shepard successfully removed the vault contents and copied the archives.
No one on either side detected the infiltration, and no faction attributed the vault or archive losses to Shepard or his forces.