The battle begins with a routine blockade over the crystal world of Christophsis. Admiral Trench commands from the Invincible, but Rain chafes under his caution, proposing a pincer move to smoke out the Republic taskforce hiding behind the moon. Trench refuses, then a cloaked ship appears and torpedoes the flagship's bridge. Trench is incapacitated, and Rain receives the fleet command codes. He seizes the moment, reorganizing the chaotic Separatist fleet into a fighting force. He uses the Munificents' unique ventral firepower to exploit the Venators' blindspot, luring Obi-Wan Kenobi's cruisers into a trap. The Republic loses two Venators, Dauntless and Resolute, in a brutal display of tactical ingenuity. Rain rescues the clone survivors, citing the Yavin Code, and cements his reputation as a commander who values both victory and humanity. The battle ends with Christophsis secured for the Separatists, but Rain knows he has made enemies and allies in equal measure.

Rain is reassigned to a covert operation with Asajj Ventress, tasked with kidnapping Jabba the Hutt's son Rotta to frame the Jedi. The mission goes awry when Luminara Unduli arrives with overwhelming force. Rain executes a daring double gravity-assist slingshot maneuver to ambush the Republic fleet, sacrificing two of his frigates to buy time. Ventress fights the Jedi on the ground but ultimately fails to secure the Huttlet. Rain captures the Padawan Barriss Offee and convinces General Tann to keep her alive as a propaganda asset rather than turning her to the Dark Side. The mission is a failure in its primary objective, but Rain gains a valuable prisoner and the trust of Sev'rance Tann. He also earns Ventress's begrudging respect, though her hatred for the Jedi remains a volatile element.

As the Republic launches Operation Trident, Rain works to build the Perlemian Coalition, a military alliance of Separatist worlds. He uses the wargame ARENA to identify reliable officers and forge bonds. He blackmails Calli Trilm, uncovers Dooku's treasonous communications with Coruscant, and manipulates the Separatist Senate to block Dooku's nominee for Supreme Commander, General Grievous. The vote fails by five votes, buying time for Tann's return. Rain's political machinations put him directly in Dooku's crosshairs, but he has built a power base that cannot be easily crushed. The Coalition now controls hundreds of warships and the swing votes in the Senate. Rain is no longer just a captain; he is a warlord in all but name.

The Republic converges on Columex with two star dreadnoughts and over two thousand warships. Rain deploys his ultimate weapon: asteroids fired from civilian freighters using tractor beams, turning them into kinetic kill vehicles. The first volleys devastate the White Cuirass Fleet. But the battle turns desperate when the Pride of the Core jumps directly above Rain's fleet, savaging the White Hand. Barriss Offee, now on a Separatist ship, witnesses the carnage and struggles with her Jedi teachings. Sev'rance Tann arrives with the Second Fleet, boarding the Pride with Decimator tanks. Admiral Trench brings the Fourth Fleet and a Separatist dreadnought. The Republic is routed, but the victory is pyrrhic. Rain's asteroid cannon nearly backfires, and the cost in lives is staggering. The battle ends with the Separatists holding Columex, but the war is far from over.