The Galactic Alliance Guard's purpose involved maintaining internal security, fighting terrorism, and law enforcement on Coruscant. Chief of State Cal Omas established the Guard as a secret police force of anti-terrorist commandos, and it operated independently of both the CSF and the GA Defense Force. Nonetheless, its personnel came from those organizations, as well as the GA Intelligence Service and its predecessor, the NR Intelligence Service. A special operations division was also part of the GAG, including elite soldiers who had served with the GA Special Forces. The Galactic Alliance Guard, under the direction of Darth Caedus, the Sith identity of the fallen Jedi Knight Jacen Solo, became a symbol of the state's approach to counter-terrorism. Black became the color associated with almost everything related to the GAG, especially the soldiers in their black plastoid armor.

The Guard's main goal was straightforward: arrest and detain anyone suspected of or confirmed to be a traitor to the Galactic Alliance. Millions of individuals, from citizens making seditious comments to Corellian terrorists and Confederate insurgents, were found guilty of treason and sent by the GAG to concentration camps. The Guard's surveillance network, which covered both civilian and government systems, made extensive use of droid technology. In addition to specially-trained GAG troopers, including spies, assassins, and special ops commandos, the Guard used a variety of droid brains and combat drones to monitor subversive HoloNet sources and put down armed uprisings. The Guard's special operations units, like the 967 Commando, were sent to different areas of the galactic capital and anywhere else anti-Alliance activities were happening. GAG troopers were equipped with a mix of riot and combat weapons, for both non-lethal and lethal purposes, depending on the mission. They also had sensor devices called Noses, attached to the back of a gauntlet, that blinked red and orange when they detected something. Their strategy involved rapid entry; dropships would enter a target zone and unload soldiers with orders to subdue insurgents and apprehend any survivors. This tactic was used consistently with little change, regardless of whether their targets were enemy combatants, unarmed protesters, neutral civilians, or hostage takers and their prisoners.

Although the Galactic Alliance Guard had access to advanced technology, its technological advantage could be turned into a weakness by ion weaponry and signal jammers. These weaknesses in the GAG's system came from the Galactic Alliance's intelligence, military, and police organizations, which had spent over thirty years fighting primitive warlords and aliens, none of whom posed a significant threat to the Alliance. As a result of not having a real rival, the Alliance became complacent and overconfident in its technology, leaving it unprepared to deal with the Confederation's anti-sensor weapons and sabotage tactics. These flaws were passed on to the Guard, which repeated the same mistakes that had jeopardized Alliance security in the first place.

Originally based in the Galactic Justice Center, one of Coruscant's many districts, the Guard was given a mobile base of operations after Colonel Jacen Solo commissioned the Anakin Solo—a modified Imperial II-class Star Destroyer named after his deceased brother—as his personal flagship. The Ninth Fleet, one of the nine Galactic Alliance fleets, was later placed under the command of the Galactic Alliance Guard.

As Darth Caedus, he used the GAG's support to seize control of the government, doing so within the bounds of constitutional legality through numerous amendments and legal loopholes. With Caedus becoming Chief of State and gaining dictatorial powers, the Guard effectively replaced the state, but it also hindered effective governance because its upper command structure was designed for overseeing infantry battle groups rather than managing the daily affairs of a galactic power.

Following a series of terrorist attacks on Coruscant in 40 ABY, Chief of State Cal Omas and Senator G'vli G'Sil led the effort to create the secret police force known as the Galactic Alliance Guard. The leadership of the Guard was initially offered to Mara Jade Skywalker, a Jedi, former Emperor's Hand, and the wife of Grand Master Luke Skywalker. When she declined due to the Jedi Order's opposition to the government's endorsement of secret police tactics, Jacen Solo accepted the leadership of the GAG, along with the military rank of colonel. However, Omas had unknowingly placed the secret police under the control of an aspiring Sith Lord, as Solo had secretly abandoned his allegiance to the Jedi by becoming the Sith apprentice of the Dark Lady Lumiya. Disgusted by the prospect of another galactic civil war, Solo had become disillusioned with the Jedi Order, which he saw as ineffective in maintaining the stability of the Galactic Alliance. He ultimately believed that the only way to achieve lasting order and peace was to embrace the dark side of the Force, like his grandfather before him, but for more selfless reasons. With Lumiya's guidance and the support of the GAG, Solo dedicated himself to building a new order at any cost.

Colonel Solo was not the only Jedi to join the Galactic Alliance Guard, despite the Order's refusal to be associated with the secret police. Much to the dismay of the Jedi High Council, Solo's thirteen-year-old cousin Ben Skywalker, son of Luke and Mara Jade Skywalker, became a junior lieutenant in the Guard. In addition to its two Jedi officers, the GAG's personnel were highly diverse; Solo handpicked numerous members from various intelligence and military organizations. Captain Lon Shevu was a CSF police officer before joining the Guard; he disapproved of the Colonel's hardline methods but remained loyal to the chain of command. Heol Girdun, another GAG officer, had previously served as an intelligence operative under the New Republic. He specialized in advanced interrogation techniques and surveillance. Corporal Jori Lekauf was the grandson of Erv Lekauf, an Imperial officer who faithfully served under Darth Vader's command. Inspired by his grandfather, the younger Lekauf joined the Guard and became one of Jacen Solo's most loyal soldiers. Despite their different past affiliations, all members of the Guard were Coruscant-born Humans—patriotic citizens of the Alliance with no association with Corellia and its fellow subversive worlds.

Shortly after its formation, various GAG special forces units were deployed throughout Coruscant's many districts, especially those with a high concentration of Corellian residents. Colonel Solo and Lieutenant Skywalker participated in several raids alongside the GAG troopers of the 967 Commando. Despite continued opposition from the Jedi Order and civilian protesters, the Guard's preemptive methods were largely successful in preventing further terrorist attacks against Coruscant. Some of the GAG's missions were recorded and broadcast on HoloNet News; many Coruscanti citizens supported their enforcement of the government's counter-terrorism policy and hailed Jacen Solo as a hero of the Alliance. However, Grand Admiral Gilad Pellaeon shared the Jedi Council's distrust of the Guard. He resigned his commission as Supreme Commander of the Galactic Alliance Defense Force because he found secret police to be a repugnant aspect of the Old Empire, which he had abolished as part of his reforms in the Imperial Remnant. Although Solo remained popular with much of the Alliance's citizenry, his critics began to compare GAG troopers to stormtroopers. For some, the Guard was a sign that the Galactic Alliance was turning into a new Galactic Empire.

Within the Guard itself, Solo was immensely popular with the rank-and-file troops, many of whom became personally loyal to him. Like Vader, Solo never gave orders that he wasn't willing to carry out himself. He preferred to lead by example, often serving alongside the GAG troopers in dangerous situations. His willingness to endure the same hardships in the ongoing fight against terrorism endeared him to the Guard. Further emphasizing his association with the Guard and his gradual disassociation with the Jedi Order, Solo abandoned his Jedi apparel and adopted a GAG uniform, complete with black robes and a cloak.

To counter the growing threat of Corellia's secessionist movement, the GAG was authorized to intern, deport, and interrogate suspects, which they did with brutal efficiency. They were also given the authority to monitor civilian activities for terrorists, insurgents, and anyone who could be considered a traitor to the Galactic Alliance. Their surveillance network extended to certain branches within the government itself, particularly the elected officials of the Galactic Alliance Senate. Colonel Solo occasionally oversaw interrogation sessions, using his Force abilities to coerce detainees into compliance. During one incident, Solo inadvertently killed a prisoner, a bounty hunter named Ailyn Vel, who had been hired to assassinate Solo and his parents, Han and Leia Solo.

Ultimately, efforts to reconcile the Galactic Alliance and the Corellian-led separatists failed, leading to the failed blockade of Corellia and the subsequent Second Galactic Civil War. Colonel Jacen Solo played an active role in the Alliance's war strategy and used the Guard's resources to undermine the Confederation's efforts to secede from the Alliance by force. Due to the expansion of the Guard's role, which had previously been limited to enforcing domestic security on Coruscant, a modified Imperial II-class Star Destroyer was commissioned as a mobile base of operations for the GAG. The starship was then named the Anakin Solo in honor of the Colonel's late brother, much to the dismay of his family.

The Anakin Solo was first deployed in combat at the Battle of Hapes, where Colonel Solo coordinated Alliance forces alongside the Hapan Military. At the same time, Han and Leia Solo were falsely implicated in a failed assassination attempt on Queen Mother Tenel Ka Djo, the leader of the Hapes Consortium and the mother of his secret child, Allana. Convinced of their guilt, and possibly believing they were meant to be sacrificed in his ascension as a Sith Lord, Solo declared them traitors to the Alliance. During the battle, he ordered one of the Anakin Solo's long-range turbolasers to fire on the Millennium Falcon. His mother's Noghri bodyguards were killed in the attack, and the Falcon sustained heavy damage before escaping his Star Destroyer through hyperspace. Solo later discovered that Dur Gejjen, the Corellian Prime Minister of the Five Worlds, was actually responsible for the attempt on Djo's life. Nevertheless, the Colonel refused to revoke the arrest warrants, choosing to keep his parents on the Guard's most wanted list because they were still guilty of initially aiding the Confederation against the Galactic Alliance.

As Lumiya continued to guide Jacen Solo through his development as a Sith Lord, the master and her apprentice considered Lieutenant Ben Skywalker as a possible future apprentice for Solo. Before making a final decision, however, they decided to test Skywalker's susceptibility to the dark side of the Force. He was sent on a covert GAG mission that eventually led him to Ziost, where Skywalker discovered a Sith Meditation Sphere known as the Ship. Upon returning to the Anakin Solo, he presented the vessel to Colonel Solo, who then gave it to Lumiya.

As the Civil War became a stalemate between the Galactic Alliance and the Confederation, Chief of State Omas and Colonel Solo became increasingly antagonistic towards each other regarding the Alliance's overall strategy. However, the crisis of rebellion worked in Solo's favor, as it motivated the Senate to pass emergency-level amendments to the Constitution, allowing the Guard's surveillance network to expand into government systems. GAG spies closely monitored high-ranking officials, including the Chief of State, and looked for any signs of treachery. The new security protocol allowed Solo to discover a secret meeting between Omas and Gejjen on Vulpter, where they discussed the possibility of a cease-fire under certain concessions, including the removal of Jacen Solo from power. Lieutenant Skywalker monitored and recorded the conversation, shortly before killing Gejjen with a sniper rifle. Before Skywalker, Shevu, and Lekauf could return to Coruscant, the GAG trio was discovered and forced to defend themselves against the Vulpter spaceport security forces. Lekauf, who had recently been promoted to the rank of lieutenant, sacrificed his life so that his comrades could escape to safety. Before his death, he claimed to be a Corellian extremist to hide the Guard's involvement in Gejjen's assassination.

Using the evidence that implicated Omas, Colonel Jacen Solo formed an alliance with Admiral Cha Niathal, who succeeded Pellaeon as Supreme Commander of the Galactic Alliance Defense Force. Like Solo, she was a political opponent of Omas and had ambitions to replace him as the next Chief of State. Through the constitutional amendments, the Galactic Alliance Guard had the authority to overthrow the Chief of State if he was proven to be a security risk to the Galactic Alliance. Colonel Solo, accompanied by two GAG troopers, Sergeant Wirut and Trooper Limm, entered Omas's office at the Executive Building on Coruscant and promptly arrested him on charges of high treason for conspiring with the enemies of the Galactic Alliance, namely the Confederate rebellion and their terrorist supporters.

With Cal Omas, the former Chief of State, confined to his residence, Solo and Niathal moved swiftly to take over the government. After calming the concerns of the senators, many of whom initially perceived the action as a military takeover, the Senate consented to the temporary establishment of a duumvirate. This arrangement involved Niathal and Solo jointly holding the Office of the Chief of State, with both being designated as Joint Chief of State Number One and Joint Chief of State Number Two, respectively. The Solo-Niathal administration gained widespread acceptance from both the government and the public, bolstered by the support of GAG and the Defense Force, ensuring a seamless and peaceful transfer of power during the coup d'état.

Shortly after Omas's removal from power, Mara Jade Skywalker confronted Jacen Solo upon discovering his clandestine connections to Lumiya's Sith Order. Ben Skywalker overheard a discussion between his cousin and the Dark Lady of the Sith, neither of whom detected the young Jedi's presence because he was employing Force stealth, a technique for masking one's own presence in the Force. Distraught, Skywalker revealed his discovery to his mother, who independently decided to present her nephew with an ultimatum: renounce the dark side and return to the Jedi Order for rehabilitation, or face death as a Sith. Solo rejected her offer without acknowledging her accusations, leading Jade Skywalker to ultimately resolve to assassinate him.

Convinced that the former Jedi was beyond redemption, she laid in wait for her nephew on Kavan. Solo retaliated in self-defense, resulting in a fierce lightsaber duel where both combatants employed a range of Force abilities and fighting styles. Her assassination attempt not only solidified Solo's commitment to the Sith, but also convinced him that his aunt was destined to be sacrificed as a crucial step in his transformation into a Sith Lord. Ultimately, Mara Jade Skywalker succumbed to a fatal wound inflicted by one of Solo's poison darts, her body succumbing to the weapon's toxin. Solo's path to becoming the new Dark Lord of the Sith was solidified, and Lumiya chose to make a sacrifice. She falsely claimed responsibility for Jade Skywalker's death, knowing that the Jedi Order would pursue her, thus affording Solo time to solidify his new position. Subsequently, she was murdered by a vengeful Luke Skywalker, who later discovered to his horror that he had killed the wrong person in cold blood.

As the last surviving member of his late master's Order, the Dark Lord of the Sith contemplated the completion of his transformation, concluding that he was no longer the same individual who had been born as "Jacen Solo." Believing himself to be liberated from his former identity, he became even more determined to establish a new era of genuine order and peace for the galaxy. After briefly observing his reflection in the black visor of a GAG helmet, the Dark Lord christened himself "Darth Caedus."

Darth Caedus, concealing his true identity behind the guise of Colonel Jacen Solo, attended the funeral of Mara Jade Skywalker at the Jedi Temple on Coruscant. Following the ceremony, he feigned interest in Luke Skywalker's proposal for reconciliation, primarily because Jedi support was essential to the Dark Lord's strategy for securing a decisive Galactic Alliance victory over the Confederation. Simultaneously, Caedus anticipated that his fugitive parents would attend the funeral, and therefore instructed a contingent of GAG troopers to infiltrate the Temple and apprehend them on sight. Despite the trap he had set for them, both elder Solos managed to evade capture by the Guard, injuring several troopers in the process.

Caedus also suspected that the Jedi Order's dedication to the Galactic Alliance's cause was faltering, and so he sought to ensure their continued compliance by occupying the Ossus Jedi Praxeum with a battalion of the Galactic Alliance Guard. Under the command of Major Salle Serpa, the GAG troopers were instructed to hold the Jedi students as hostages. Jaina Solo, Caedus's twin sister, realized that the Guard's presence was not to provide security for the Praxeum, but rather to eliminate the students if the Order became disloyal. She also suspected that Serpa had been chosen to lead the GAG task force because of his personal loyalty to the Colonel and his eagerness to kill all of the Jedi on Ossus.

Meanwhile, the Anakin Solo spearheaded the Galactic Alliance Fifth Fleet in the defense of Balmorra. The battle was a fiercely contested conflict for both Alliance and Confederate forces. However, the Confederation's naval strength was augmented by a military alliance with the Hutts, leaving the Alliance in a precarious position despite Caedus's use of battle meditation. With victory uncertain, Caedus ordered his fleet to inflict as many casualties as possible on the enemy, thereby hindering their ability to support other Confederate forces at Kuat. His tactics, however, including his willingness to sacrifice Balmorra, were morally reprehensible in the opinion of the Jedi.

Darth Caedus's plan to secure the Civil War with an Alliance victory depended on utilizing Luke Skywalker's squadron of Jedi StealthX wing starfighters against the Confederate fleet. By eliminating the rebellion's military capabilities, Caedus believed that rebels would no longer be able to sustain their cause. Yet when Skywalker discovered that the Order's Ossus facility had been occupied by the Guard, the outraged Grand Master recalled his squadron and abandoned the Dark Lord in the middle of the Battle of Kuat. The Alliance gained a hard-fought Pyrrhic victory, but failed to achieve the decisive the final victory that Caedus had hoped for. Enraged by their actions, Caedus directed his forces in pursuit of the Jedi to the Wookiee homeworld of Kashyyyk.

As a consequence of Skywalker's desertion of Caedus at Kuat, all Jedi were labeled as traitors to the Galactic Alliance. The Guard dispatched armed troops to the Temple on Coruscant with orders to subdue its occupants and secure the facility. The Jedi fought back, repelling GAG troopers at the main entrance until the Order's evacuation was complete. The Jedi then dispersed into hiding, leaving the Temple to GAG occupation. On Ossus, Major Serpa was ordered by Caedus to eliminate the Jedi Praxeum's inhabitants with lethal force if necessary. The Guard deployed coma gas into the dormitory rooms of the adult Jedi, but Jaina Solo managed to escape from the effects of the gas. The rest of the Jedi were herded into the Praxeum's central exercise pavilion by GAG troopers. Jedi Master Tionne Solusar threatened Serpa to stand down, but only succeeded at providing the Major with an excuse to shoot her in the leg. Master Kam Solusar tried to rescue his wife, but was shot three times by GAG snipers. Jaina Solo and Jagged Fel subdued the remaining snipers by then, and led the students in a counterattack against the Guard. In the ensuing fight, many GAG troopers were defeated by the Jedi's Force abilities; Serpa fought off several Jedi, but was severely injured after his arm was severed by the Jedi Zekk's lightsaber. The remaining troops, disgusted by the Major's brutality, subsequently surrendered to Solo.

Amidst the setbacks on Coruscant and Ossus, Darth Caedus's fleet arrived at Kashyyyk where he demanded the Wookiees to release Skywalker and the Jedi into Alliance custody. Knowing that the proud warrior race would not likely comply, the Dark Lord seized the opportunity to demonstrate the consequences of committing acts of treason against the Galactic Alliance. By that time, Ben Skywalker resumed his place at Caedus's side, but—convinced that his cousin was responsible for Mara Jade Skywalker's death—secretly intended to assassinate him during the fight. At the young Skywalker's suggestion, Caedus used the Anakin Solo to launch an orbital bombardment on Kashyyyk, resulting in a massive firestorm that incinerated many Wookiee settlements, including the city of Rwookrrorro. Amidst the chaos, Skywalker moved to strike Caedus down, but failed and instead accidentally killed Commander Twizzl. Caedus was pleased by his young cousin's initiative, and interpreted it as a sign that Skywalker could still be turned to the dark side of the Force.

Skywalker was subjected to the Yuuzhan Vong Embrace of Pain and tortured by his former mentor until Luke Skywalker arrived after infiltrating the Anakin Solo. The Jedi Grand Master and the Dark Lord of the Sith engaged in a duel, resulting in Darth Caedus being brought near to death. The elder Skywalker refrained from killing his nephew, however, because of his fear that the desire for revenge would lead him and his son to the dark side. Both Skywalkers escaped from the Star Destroyer, leaving Caedus to recover from his injuries while attempting to direct his remaining warships against the combined forces of Jedi, Wookiees, the Confederation, and the Hapes Consortium, which by then had also rebelled against Alliance authority. Although Darth Caedus and his fleet were forced to flee from Kashyyyk, the Jedi—including their Wookiee and Hapan allies—refused to join the Confederation. Instead, the Order formed a coalition with a specific agenda to eliminate Darth Caedus; unlike the Confederation, secession from the legitimate state was not their goal. In retaliation for Tenel Ka Djo's treachery, Darth Caedus abducted their daughter and kept her on the Anakin Solo, where she would be under heavy GAG protection. He threatened to kill Allana unless the Hapan Consortium reaffirmed its allegiance to the Galactic Alliance.

The Galactic Alliance Guard later defended Darth Caedus on Coruscant when a Jedi strike team, led by Master Kyle Katarn, ambushed the Dark Lord and his military escort in the Underworld of Galactic City. Their first action was to incapacitate the GAG troopers by temporarily blinding them with dazzle-grenades. The Jedi were instructed to capture or kill the Dark Lord if necessary, but Caedus proved too formidable an opponent. He single-handedly defeated his opponents one at a time, and nearly killed Katarn with a lightsaber strike through the torso. By that time, reinforcements arrived just as the GAG troopers were regaining their sight. The remaining Jedi retreated, but not before Seha Dorvald telekinetically planted a homing beacon on Caedus's cloak. The device was later discovered by Lieutenant Patra Tebut, a GAG officer who served as part of the Anakin Solo's bridge crew. Impressed by the young woman's loyalty and efficiency, Caedus told Captain Kral Nevil to place a commendation on Tebut's permanent record.

The Guard served alongside the GA Defense Force, under the command of Darth Caedus, at the Centerpoint Station, in which the Galactic Alliance, the Confederation, and the Jedi Coalition fought each other for control of the space facility. A team of GAG troopers and elite commandos was deployed to capture Centerpoint Station, but ultimately failed in their task when Rikel, a disgruntled civilian who blamed GAG for his wife's death, inadvertently destroyed the station while attempting to direct the facility's destructive capacity toward Coruscant. The explosion of Centerpoint Station destroyed numerous starships, killing many Alliance and Confederate troops in the process. Both Caedus and the Anakin Solo, however, were beyond the blast radius.

During the chaos of the battle, Allana had been rescued from captivity by the Jedi Coalition. Upon realizing that she was no longer on his flagship, the Dark Lord rushed to the bridge and demanded an explanation. Lieutenant Tebut confessed that she unwittingly allowed a Jedi team to land in the Anakin Solo because they had transmitted the proper codes for docking procedures. Caedus, overwhelmed with rage, seized Tebut in a Force Grip and began choking her. Tebut pleaded for her life, professing her loyalty to Caedus. Captain Nevil tried to save the Lieutenant, but was swiftly shoved aside by a powerful Force Push from the Dark Lord. Accusing her of gross insubordination and gross misconduct in the field, Caedus Force Choked Tebut to death, and then slammed her on the ground, breaking numerous bones in her body. The entire bridge crew was stunned and far too petrified with fear to do anything except watch in horror as their Colonel murdered his subordinate in a manner resembling Darth Vader's preferred method of execution for incompetent officers.

In the weeks following Tebut's death, Caedus eventually came to regret his outburst. Once his anger had subsided, he was shocked by his own actions and, for a while, he sometimes forgot that Tebut was no longer alive. He realized that her mistake was understandable and due to unforeseen circumstances that were beyond her control. In addition to the loss of a reliable officer, Caedus understood that his act of murder had traumatized the men and women who served under him.

As word spread of Tebut's death, and the manner in how it happened, many within the Galactic Alliance Guard were conflicted, confused and unsure of how to respond to such an unexpected move by their leader. Some troopers, such as Nevil and Shevu, lost their respect for Caedus, while others pragmatically acknowledged that he was the most effective commanding officer that they ever had. Though he was further disappointed in himself for failing to manage his anger, Caedus ultimately viewed Tebut's death as a sacrifice that would force him to learn how to be a better and more responsible Sith Lord. He later confided in Captain Nevil about his regret over killing Tebut and tried to assure the GAG officer that he had nothing to fear; Nevil dutifully acknowledged his superior officer and continued to obey orders, but by then his loyalty to Caedus had been destroyed.

Darth Caedus, having judged his cousin Ben Skywalker as a lost cause to the Sith, began to grudgingly transfer his expectations to the Jedi Knight Tahiri Veila. Although he originally intended to use her as a spy by taking advantage of her attachment to his deceased younger brother, Caedus steadily became more impressed by Veila. In order to further test her willingness to embrace a new life apart from the Jedi Order, Caedus brought Veila with him as the Anakin Solo traveled to Fondor, a planet that had betrayed the Galactic Alliance by siding with the Confederation. Upon reaching the planet, several Fondorian starfighters steadily approached the GAG Star Destroyer. Caedus then ordered the bridge crew to deactivate the vessel's shields, at which point he presented Veila with two choices—give the order to have the Anakin's weapons destroy the starfighters before they could attack, or withhold fire and risk getting many GAG personnel killed if the Fondorians chose to make the first strike. Veila hesitated at first, but then gave the order to kill the approaching enemy fighters. Once the Anakin Solo returned to Coruscant via hyperspace, Admiral Cha Niathal was displeased that her colleague had placed a military warship under the command of a civilian, despite the fact that Veila was a trained Jedi. At Niathal's suggestion, Caedus officially recruited Veila into the Galactic Alliance Guard, bestowing the rank of junior lieutenant upon her.

During the Second Battle of Fondor, the GAG fought alongside the Galactic Alliance Defense Force, led by Admiral Cha Niathal, and a naval fleet of the Imperial Remnant, headed by Admiral Gilad Pellaeon. Utilizing the Force, Darth Caedus taxed the extent of his powers to deactivate Fondor's planetary shield. With the enemy's primary defense nuetralized, the Anakin Solo led the cavalry charge through the Fondorian starships in order to unleash a bombardment on the planet's surface. But while Caedus was distracted by leading the attack, Niathal undermined her colleague's plan by unilaterally accepting Fondor's surrender. In an underhanded attempt to force the Sith Lord out of power, or to at least exert her authority over him, Niathal ordered Caedus to cease and desist with his offensive strike against Fondor. Betrayed once again, Caedus denounced Niathal as a traitor, declared himself as the sole Chief of State and commanded the Alliance fleet to continue the fight. Niathal, in turn, declared Caedus a traitor and ordered the fleet to acknowledge her as its sole commander-in-chief.

As internal chaos and utter confusion erupted due to the sudden collapse of the duumvirate, the Galactic Alliance Defense Force began fighting itself as various starships declared for either Caedus or Niathal. Pellaeon, an openly hostile critic of Caedus, declared his support for Niathal and directed the Imperial vessels to accept only her orders. Lieutenant Tahiri Veila, who had remained with Pellaeon on the Bloodfin as Caedus' liaison, tried to convince Pellaeon to not destroy the Galactic Alliance by betraying Caedus. When he refused, Veila fatally shot the Imperial Head of State through the chest. With Pellaeon dead, the senior members of the Moff Council assumed leadership of the Remnant and declared their support for Caedus, and thus commanded the Imperial fleet to fight alongside the forces of the true and legitimate Galactic Alliance.

About two-thirds of the Defense Fleet threw their support behind Darth Caedus; the entire Galactic Alliance Guard itself remained loyal to its leader. By comparison, there was only a small minority of deserters that composed Niathal's faction. Thus, Niathal's scheme to overthrow her Joint Chief of State ultimately backfired. Although she knew that the GAG would never side with her against its colonel, she made a great error in judgment by underestimating Caedus' popularity within the military, as well as overestimating her own chances of assuming sole leadership simply because of her rank as an admiral.

Much of the crew of the Bloodfin, however, was personally loyal to the late Pellaeon. The quick discovery of his assassination caused many Imperials to initiate a mutiny against the Moffs, all of whom had barricaded themselves on the bridge with Tahiri Veila. Contacting Veila from the Anakin Solo, Caedus congratulated the GAG lieutenant for single-handedly saving the entire Galactic Alliance. When Veila admitted her lack of enthusiasm in killing an old man, Caedus absolved her of the guilt that she felt and declared Veila as his Sith apprentice. At that point, he decided that he would be known only by his true name from that point on, thus dropping his facade as Jacen Solo once and for all. Refusing to lose his apprentice after finally discovering the right one, Caedus risked his own life by infiltrating the Bloodfin in a move to retrieve Veila. Although the Sith Lord and Lady sustained injuries during the rescue attempt, Caedus ultimately succeeded in bringing Veila back to the safety of the Anakin, where he realized that they were destined to rule together as master and apprentice. Afterward, the Alliance and Remnant forces withdrew from Fondor. Although the battle was considered a defeat, the loss of Fondor was inconsequential to Caedus since the Rule of Two had been restored with Veila's ascension to the only remaining rank within the Sith Order.

Returning to Coruscant, Caedus officially established himself as the sole Chief of State of the Galactic Alliance—his rule enforced by the GAG presence on the galactic capital. When Captain Shevu arrived in Caedus' new office, his report turned into an informal conversation in which Caedus revealed how he killed Mara Jade Skywalker and assumed his mantle as the Dark Lord of the Sith. Unknown to him at the time, however, Shevu had become a spy within the Galactic Alliance Guard for the Jedi Order. After secretly recording the conversation, he sent it to Ben Skywalker as proof of Caedus' direct involvement in Mara's death.

At some point, the Guard were engaged in combat against a Kel Dor Sith Lord.

In late 41 ABY, Captain Shevu met secretly with the Jedi Ben Skywalker, Leia Organa Solo and Jaina Solo On Coruscant to report on the activities and whereabouts of Chief of State Darth Caedus. However, during the meeting, the Jedi were followed by two Rodian informants of the Galactic Alliance Guard. Skywalker feigned an altercation with Shevu and gave the impression of resisting arrest, primarily so that Shevu could remain on Coruscant as the Jedi's spy.

As he attempted to flee the area, his path was obstructed by the Sith Lady Tahiri Veila, who was clad in GAG armor and a black cloak, thus mirroring her master's appearance. An elite team of GAG commandos trailed closely behind Veila. Skywalker briefly engaged the Sith apprentice in a lightsaber duel until a squad of GAG troopers opened fire on him. While preoccupied with redirecting their blaster bolts, Skywalker was rendered unconscious after being struck several times in the back by Veila. Simultaneously, Shevu was overwhelmed and apprehended by his former GAG comrades.

Once Veila and her shock troops loaded Ben and the prone Shevu into a Doomsled, Jaina made her way over to Leia, noticing the two Rodians being loaded into a med-wagon. Using a few acting tricks and some Force Force suggestions on CSF officers Tobyl and Jat'ho, the Solos commandeered the med-wagon. Ejecting the hapless Bith pilot, they took to the skies after Veila. Going a different way initially, to throw off suspicion, once they were out of sight of the GAG troopsleds, Jaina shoved the throttle forward, and they sped after the Doomsled.

As they closed in on the GAG squad, Leia ensured the two Rodians in the medical transport remained unconscious by administering additional sedatives upon their awakening. Leading the way, Veila guided the Jedi closer to the Galactic City SpeedPipe, but a growing unease settled upon them as they suspected a potential ambush. Their fears were validated when Veila, having anticipated the rescue mission, activated a gas trap with a voice command. Jaina and Leia managed to evade the gas through their resourcefulness. With the GAG firmly in control of the capital world, they made the difficult decision to abandon Skywalker and flee Coruscant.

Not long after, Ben Skywalker was subjected to repeated torture during an interrogation conducted by a GAG security droid identified as SD-XX. Although the droid failed to extract any information about the Jedi Order's clandestine base, its methods were successful in severely weakening Skywalker's mental defenses, thereby creating an opportunity for Tahiri Veila to assume control of the interrogation. Dressed in a skin-tight GAG jumpsuit, Veila attempted to seduce the young Jedi prisoner by feigning compassion and tending to his wounds. Despite Skywalker's understandable temptations, compounded by his fear of SD-XX's interrogation techniques, he resisted Veila's advances by reminding himself that she was the Sith apprentice of the one responsible for his mother's death.

Veila then shifted her strategy, threatening the life of Lon Shevu, whom she attacked with Force lightning. However, she inadvertently killed the former captain, having underestimated the potency of her own dark side abilities. As she attempted to revive Shevu, Skywalker seized the opportunity created by her distraction to break free from his restraints. He then incapacitated Veila by throwing her into her GAG guards, rendering her unconscious, and successfully escaped from Coruscant.

Just prior to the last battle of the war, Darth Caedus and Tahiri Veila finally discovered the location of the Jedi Order's hidden base on the planet Shedu Maad. Leading the Anakin Solo and a small fleet of Imperial warships in a final attempt to eradicate the Jedi insurgents, the Sith Lord's forces were surprised by the Jedi's fierce resistance and counteroffensive. While Veila commanded a squad of Imperial shock troopers from the Moffs' Elite Guard, Jaina Solo boarded the heavily damaged Anakin to confront and eliminate her twin brother. As the GAG suffered significant casualties alongside the rest of the Alliance fleet and their Imperial allies, Caedus met his end at the hands of Solo in a duel to the death. Veila, by this point disillusioned with her master, surrendered and was taken into Jedi custody.

Lacking strong leadership to reverse their failing fortunes, the remaining GAG troopers who had accompanied Darth Caedus were trapped aboard the Anakin Solo and were compelled to surrender to the victorious Jedi Coalition. Following the battle, the Confederation also conceded defeat to the combined might of the Galactic Alliance, the Imperial Remnant, and the Jedi Order. With the conclusion of the Second Galactic Civil War, the Galactic Alliance Guard was dissolved, and its former leader was succeeded by Natasi Daala, formerly of the Imperial Remnant, as the new Chief of State of the Galactic Alliance. Many of the former GAG's responsibilities were transferred to the newly established Galactic Alliance Security (GAS). As the galaxy began to return to a semblance of peace, many of the surviving members of the GAG were forced to operate covertly within Daala's government, while continuing to harbor a particular resentment towards the Corellians.

The Galactic Alliance Guard was conceived for the Star Wars: Legacy of the Force series, which commenced publication on May 30, 2006 with the novel Legacy of the Force: Betrayal. It made its initial appearance in the novel Legacy of the Force: Bloodlines, released on August 29, 2006. The GAG's behavior becomes increasingly more violent as the series progresses. Galaxy of Intrigue, published on January 19, 2010, officially confirmed the organization's disbandment.