The Meridian Complex assault represents a pivotal and conclusive engagement during the renewed conflict between the Sith Empire and the Galactic Republic. The Empire initiated a substantial fleet offensive against the Republic planet of Corellia, with the primary objective of obliterating the advanced Meridian Complex shipyard.
As the third Galactic War commenced, the naval capabilities of the Republic were challenged to match the Sith Empire's, which had experienced a significant resurgence under the leadership of Empress Darth Acina after enduring setbacks during the Eternal Empire conquest. A Republic strategic group successfully engineered a massive shipyard on Corellia, known as the Meridian Complex, designed to produce starships at three times the rate of Imperial shipyards and with half the energy consumption.

The Empire became aware of the shipyard's existence through intelligence gathered by Darth Xarion's operatives within Sith Intelligence, immediately designating it as a high-priority target to neutralize before it could become fully operational. Darth Krovos and Darth Malgus assembled a considerable armada for the attack by consolidating their frontline forces and redeploying nearly all but the most essential warships, along with sufficient fuel transports to enable the Imperial fleet to jump directly to Corellia without the need for intermediate refueling.
General Ardinondu Dipolus Daeruun received intelligence regarding the Empire's forthcoming assault and promptly mobilized all available Republic fleets to defend Corellia. Regrettably, the Eleventh Fleet and the Twenty-Ninth Fleet were required to make refueling stops at Onderon and Mek-Sha, and Daeruun anticipated potential sabotage attempts by the Empire's elite agents. Concurrently, the Commander of the Eternal Alliance arrived to bolster the Republic's defensive capabilities.

As hostilities commenced, the Empire deployed two fleets under Malgus's command, featuring dreadnoughts equipped with Silencer technology and vessels carrying isotope-5, which directly engaged the Republic fleet. Simultaneously, a third fleet, led by Krovos, emerged from hyperspace on the opposite side of Corellia, initiating orbital bombardment of the planet's surface in an attempt to divert Republic forces from the main battle. Amidst the chaos, Malgus spearheaded several shuttles, initially concealed by the isotope-5 ships to evade Republic sensors, towards the planet's surface, initiating a ground assault on the Meridian Complex. By the time the Republic ships became aware of the situation, engaging Malgus's landing party would have risked friendly fire.
The Alliance Commander directed the Alliance fleet to engage Krovos's fleet. Landing on Corellia, the Commander, accompanied by Jedi Knight Tau Idair and Padawan Arn Peralun, pursued Malgus towards the Meridian Complex. Upon encountering Tharan Cedrax, he revealed to his rescuers that he had rerouted the facility's shield controls to an auxiliary station located near the spire's summit. The trio then ascended to the spire's peak, where they confronted Malgus, who had already deactivated the shields. Following an intense duel, a defeated but impressed Malgus acknowledged the veracity of the rumors surrounding the Commander's defeat of Vitiate. Refusing to concede, Malgus used the Force to bring down an overhead machine onto the platform, causing it to collapse. While Idair and Peralun reached safety, the Commander leaped across the gap to the auxiliary station and restored the shipyard's defenses, which began targeting the Imperial fleet, compelling Krovos to order a retreat. Malgus also managed to escape, with Daeruun observing that no ships were retreating towards Imperial space.

Aboard Carrick Station, the Commander received an invitation to join Task Force Nova, a collaborative military-civilian endeavor aimed at reunifying the Jedi Order and establishing a new homeworld for them. Furthermore, Supreme Chancellor Galena Rans formally extended an offer to integrate the Alliance and Odessen into the Republic, guaranteeing amnesty and citizenship for members with criminal records or non-Republic origins. The Commander accepted after deliberation, and the Alliance was officially incorporated into the Galactic Republic.
The victory on Corellia acted as a source of inspiration for the Republic, significantly boosting morale and reaffirming its strength on the galactic stage following the Eternal Empire's occupation. Consequently, Republic forces launched offensive operations, achieving significant advancements in the Atrivis, Bormea, and Anoat sectors.
Should the player remain loyal to the Empire, the Republic's naval strength would be severely diminished due to the sabotage operations conducted on Onderon and Mek-Sha, potentially leading to the elimination of both the Eleventh and Twenty-Ninth Fleets. Before the assault, the Commander can either encourage Darth Krovos to minimize civilian casualties and prioritize key targets, earning light side points, or endorse her indiscriminate bombardment of Corellia.

During the ground assault, the Commander collaborates with Major Anri to reach the Meridian Complex, where they confront Tharan Cedrax, who discloses that Tau Idair redirected the shield controls to the spire's summit before destroying the primary controls. As Malgus arrives, the Commander can choose to execute Cedrax, take him as a prisoner, or instruct Anri to use him as a human shield.
The Commander and Malgus then engage Idair and a squad of Republic troopers in combat. After defeating Idair, the Jedi desperately triggered the collapse of an overhead machine onto the platform. The Commander succeeds in reaching the auxiliary controls and lowering the shields, allowing the Imperial fleet to destroy the Meridian Complex.
In the aftermath, the Commander attends a meeting of the Dark Council on Vaiken Spacedock. Darth Xarion reports that the destruction of the Meridian Complex has forced the Republic to withdraw from numerous worlds, enabling Krovos to initiate invasions and claim the most valuable territories within weeks.
As the Dark Council is dismissed, Empress Acina (or Emperor Vowrawn, depending on the Commander's allegiance during the War on Iokath) concludes that the council is better suited for administrative duties rather than critical wartime decisions. Consequently, the task would be assigned to a new Emperor's Hand, staffed not by murderous fanatics as with its predecessor, but by the Empire's most capable and loyal frontline personnel, particularly candidates from the Alliance. The Commander is also invited to rejoin the Empire, with Alliance members gaining full citizenship. Sith Warrior players can reclaim their title as Empire's Wrath; Sith Inquisitor players can regain their seat on the Dark Council and all their past holdings; Bounty Hunter players can simply gain the title of Hunter for the purpose of hunting down the Empire's enemies; and Imperial Agent players can attain the rank of Keeper and manage intelligence operations independent of Xarion's Sith Intelligence. Alternatively, the Alliance can maintain its independence while collaborating more closely with the Hand than the Dark Council.

Separately, while Malgus was under medical observation, a medical droid removed the explosive implant used to control him, much to the Imperial doctor's dismay. The droid noted that, unlike the other damage Malgus had sustained, the implant had been damaged by a high heat implement. Malgus then regained consciousness and drew his lightsaber, demanding both the droid and a ship.