Outer Rim – Covert Operation: Black Eclipse
The mission to retrieve Dr. Shepard was designated Black Eclipse.
Led by Obi-Wan Kenobi and Anakin Skywalker, the operation involved two Venator-class Star Destroyers, three battalions of elite clones, infiltration teams, and a fleet of LAAT gunships.
Intel provided by a captured Neimoidian had narrowed Shepard's location to a hidden Separatist outpost within a volcanic asteroid field orbiting Vharzun.
The base was defended by hybrid droid systems upgraded MagnaGuards, automated flak stations, seismic mines, and shielded hangar platforms. The Separatists were expecting a fight.
And they got one.
The Battle for Shepard
Clone Commandos from the 212th Attack Battalion breached the external hangar. LAATs rained fire. Jedi-led detachments carved through droids. The asteroid shook under the thunder of orbital bombardment and thermite charges.
Obi-Wan led the main charge.Anakin dove deep into the core with his own squad, intent on retrieving Shepard himself.
It was chaos.
Room by room, hallway by hallway, they fought.
It took six hours of non-stop conflict to reach the central command vault. And when they did, Shepard was standing there calm, unshaken.
Count Dooku – The Shadow Exchange
Hours earlier, deep in the base…
Count Dooku had entered Shepard's holding chamber.
The two men stood in silence.
One, a former Jedi Master turned leader of the Separatists.The other, a quiet architect of war playing all sides, yet bound by none.
"You don't belong to them," Dooku said softly. "Join me. I offer freedom. You and I can end this war in weeks."
Shepard studied him, his gray eyes unreadable.
"The Republic wants to win a war. The Jedi want to survive it. You want to replace the system. But me…"
He smiled.
"I want to own the system that comes after it."
Dooku frowned, sensing the depth of the man's ambition but not the whole of it.
"Then we are alike."
"No, Dooku. I make things. You just destroy them."
Moments later, the wall exploded, and Anakin Skywalker burst through in a storm of rage, cutting down droids with brutal precision.
The Rescue and the Fallout
They extracted Shepard… but at great cost.
Out of the 9,000 clone troopers deployed, over 3,400 were killed or left behind.
As the Republic fleet retreated under Separatist pursuit, Anakin turned on Shepard in the main hangar of the Resolute.
"You better be worth it," Anakin growled, bloodshot eyes fixed on him. "Thousands died pulling your ass out. And you don't even flinch?"
Shepard blinked, then responded coldly:
"Yes. They died. That is exactly what they were created to do."
"You heartless"
"You think I gave them names? I gave them functions. If you have a problem with that, talk to your Republic. I'm just the man building what it asked for."
The silence afterward was deafening.
Obi-Wan stepped between them.
"That's enough, Anakin."
He turned to Shepard, more composed.
"We're grateful you're safe. But perhaps… next time, a distress beacon might help."
Shepard said nothing.
Anakin stormed off.
Coruscant – Reinstated and Funded
Once back, Shepard was quickly restored to his position by direct order of the Chancellor.
The Kaminoans protested, but Palpatine overruled them. Shepard had become indispensable—the only one who could stabilize and innovate the clones on the scale the war now demanded.
At the next Military Oversight Council, Shepard stood before the Republic's war advisors.
"I can double output. But if you want them grown in fifteen months instead of twenty-four, the physiological risk increases exponentially. And so does the cost."
Palpatine leaned forward.
"How much?"
"1.9 trillion credits for the first wave. More later."
"Approved."
Genesis Protocol – The New Clone Doctrine
With full budgetary control, Shepard enacted the Genesis Protocol:
Clone growth reduced to 15 months
Mental development accelerated using sensory neural overlays (non-AI, bio-composite)
Select gene templates altered for increased resistance, combat reflexes, and squad cohesion
Emotional inhibitors rebalanced to prevent field hesitation—but maintain tactical creativity
For every fallen trooper on Vharzun, ten more were already growing.
And Shepard?He was already calculating how many more he'd need to reshape the galaxy.