The Trooper landed on Ord Mantell as a new sergeant just transferred to Havoc Squad, a special forces unit. On their way to headquarters, they met Havoc Squad member, Gearbox and several other Republic Troopers where he/she is briefed about the ZR-57 Orbital Strike Bomb .The walker was then hit by an anti-vehicle missile launched from inside the nearby Drelliad Village, and the Trooper was assigned to find caches of shoulder-fire missile launchers and destroy them. The Trooper then completed the task and went to Fort Garnik where they met the other Havoc Squad members Commander Harron Tavus, Wraith , Needles, and Fuse, along with a Republic operations officer named Lieutenant Aric Jorgan. The Trooper followed the intel on finding the bomb, and Havoc Squad went a head to the separatist to retrieve it. When they did not report in, The Trooper went to retrieve the bomb and save them. The Trooper found Havoc Squad colluding with Imperial officers, defecting to the Empire and stealing the bomb before fleeing the planet. When the Trooper returned to headquarters, they found Jorgan being demoted by a general as a scapegoat for Havoc Squad's defection, and the Trooper got promoted to lieutenant as the leader of the new Havoc Squad and Jorgan was made the first member of the new team. They took a shutter and headed to Coruscant.
Reaching Coruscant, the Troopr and Jorgan met with General Garza. She ordered them to stop the gangs, the Back Suns and the Migrant Merchant's Guild, from supplying the treacherous Havoc Squad. The Trooper stopped the Migrant Merchant's Guild, and with the help of a Sergeant named Ava Jaxo the they stopped the Black Suns. The Trooper was called in to meet with members of the Senate about Havoc's defection, before returning to duty. Garza discovered that former leader and founder of Havoc Squad, Jek Karden, was serving as a member of a mercenary group and working to help the traitors and the Imperials. The Trooper defeated the veteran, and discovered a communications relay which Havoc Squad used to communicate and it was discovered the traitors were located on four different planets. Before heading out, the General revealed Wraith had kidnapped a Senator and provided the Trooper with a ship to track her and the rest of Havoc Squad down.
Chapter 1 (The Hero of Havoc)
The Trooper tracks down Wraith's space station where she's rigged the Senator with explosives and the Trooper had to choose whether the track down and kill Wraith or save the Senator. After the hostage situation is settled, the Trooper is given the first two cordinates to Taris and Nar Shaddaa.
On Taris, the Trooper met with Republic Sergeant and Imperial defect, Elara Dorne, who informed them about missing teams. Finding one of the missing teams, Havoc Squad learned the one behind the disappearances was one of the traitors, Needles. Following the leads, they discovered Neeldes was experimenting to create a weaponized rakghoul disease. Taking Dorne's advice, the Trooper located Needles, and his rakghoul allies, and killed them. After returning to update Dorne, the Trooper contacts Garza to update her on the situation. For her excellent service, Dorne is placed into Havoc Squad.
Arriving at Nar Shaddaa, Garza informed the Trooper of an experimental droid commiting crimes across the planet, believed to be acting orders under Tavus. Meeting with SIS agent Jonas Balkar, they track down the droid, M1-4X, who, while still faithful to the Republic, was under the direct control of Tavus's ally, Captain Andrik, and the two escaped. With Balker's help, the Trooper was able to track them down again. The Trooper killed Andrik, and with some advice from M1-4X, were able to destroy the droid. M1-4X is repaired and becomes the next member of Havoc Squad.
Garza contacted Havoc Squad on the ship, telling them that Tavus stole a cloaking device with a tracker and they located his ship. Boarding the ship and circumventing the traps, Tavus contacted the cloaked ship, via holo, and told them it was a trap. The Trooper killed the squad, Imperial Shadow Fist and retrieved the cloaking device. After updating Garza, the general informed them of the final two planets: Tatooine and Alderaan.
One of the traitors was located on Tattoine, with the city, Anchorhead, suffering from bomb attacks. The Trooper and Anchorhead's mayor were contacted by the traitor, Fuse, who regretted defecting and tried to help the Trooper stop the Imperials from using his weapons. He led the Trooper to Geonosians who were building the bombs. Fuse helped the Trooper find a way to locate the Imperial base and the Trooper arrived as the base was being evacuated with the bomb plans and set to self-destruct with Fuse still imprisoned in a cell. The Trooper completed the mission, stopping any future bombings on Anchorhead and left Tatooine.
On Alderaan, Garza informed the Trooper that a captive member of House Thul had information on the traitor, Gearbox. After interrogating the prisoner, the Trooper made a deal with the prisoner to save his family, in exchange for Gearbox's plans and location. After rescuing his family, the prisoner revealed Gearbox's base of operations. The Trooper arrived and found Gearbox created a giant robot, which he piloted. After the trooper destroyed the robot, Gearbox was ejected from the machine and fought the Trooper to the death. Afterwards, the Trooper decided the fate of the prisoner and left the planet. After the mission, Garza called the Trooper back to Coruscant for the final mission against the remaining Havoc Squad traitor, Tavus.
Havoc Squad met with Garza, who used the communications of the four planets to locate Tavus on the ship, the Justice. Havoc Squad infiltrated the ship and defeated of what remained of the treacherous Havoc Squad.
Chapter 2 (Threats in the Darkness)
Some time after dealing with the defectors, Havoc Squad was contacted by General Garza for an important assignment. First, Havoc Squad was rewarded for their service, and the Trooper is promoted to Captain while one of their companions was promoted to lieutenant. Garza informed the Trooper of an Imperial superweapon known as the Gauntlet. The Trooper was sent to Tatooine and extracted an undercover SIS agent who informed them of the Gauntlet's capabilities to fire on a ship through hyperspace. They discovered the Empire is planning on mass producing the Gauntlet weapon and the prototype needed to be destroyed. Havoc Squad was tasked with destroying it, but first it needed a technical specialist and an explosives expert. They needed to get the first recruit on Balmorra.
Arriving on Balmorra, the General informed Havoc Squad they needed to find a Weequay named Tanno Vik, who was dishonorably discharged from the army. However, he's the best explosives expert and Havoc Squad needed to recruit him.They landed on the planet and heard that Vik was on a "mission". In Sobrik, the Trooper made holo contact with Vik, who had the Trooper work to help his goal in getting into a vault. Vik was kidnapped by the Imperials and rescued by Havoc Squad and he helped the Trooper reach the vault with Balmorran weapons which Vik wanted to steal and sell. After retrieving the weapons, the Trooper got Vik as the next member of Havoc.
Arriving on the ship, Garza sent the Trooper to Quesh to save a platoon known as "Safecrackers", who were vital in the plan to assault the Gauntlet. After the rescue, the Trooper is sent to Hoth for the final member of the team.
One Hoth, the Trooper needed to recruit a tech. expert, Gand named Sergeant Yuun. Yuun was gather materials from crashed Imperial ships to piece together an Umbra encryter, which would gain access to Imperial codes. Some Umbra components were taken by White Maw pirates and the Trooper retrieved it from them. The Trooper is able to assist Yuun in completing the Umbra encrypter and Yuun joined Havoc Squad for the assault on the Gauntlet.
Once Havoc Squad was assembled, Garza informed them on the Guantlet and how to destroy it. The Safecrackers would bring down the shields and Havoc Squad could infiltrate it. Once aboard, Yuun was able to bypass security on the ship, and Vik planted explosives around the ship, while two members assaulted the bridge to retrieve data and acted as backup. Havoc Squad evacuted the ship, with one member seriously injured and the Guantlet is destroyed. The Trooper is promoted and is contacted by Imperial General Rakton who promised retribution for the Guantlet's destruction.
Chapter 3 (The Galaxy at War)
On the ship, Garza told the Trooper Rakton invaded several Republic planets and captured their leaders. Havoc Squad infiltrates the base and rescues to hostages. When the Trooper returned, they were instructed to gather valuable troops to fight for the Republic.
On Belsavis, the Trooper is tasked with recruiting Dagger Wing, disavowed Republic pilots sentenced to Belsavis for their part in attack and Imperial planet, risking the break in the Treaty of Coruscant. The Trooper found out Dagger Wing was scattered around the prison, trying to help the Republic retake the prison. While gathering the pilots, the Trooper learned Dagger Wing was trying to kill a Sith Lord, but with bad intel, they killed civilians and they were sentenced to Belsavis. The Trooper discovered the CO found the Sith Lord originally targeted by Dagger Wing to be on Belsavis and the CO was trying to catch him to clear their name. The Trooper found the captain and their mission was completed on Belsavis, leaving the planet with Dagger Wing.
When Havoc Squad returned to the ship, they had to take on a special mission to rescue prisoners of war. One of the prisoners, Jaxo, sent a message of a prison at A-77. They reach the prison to find it was a trap by Rakton who sent ships to destroy the prison. Saving the prisoners who involve increasing the shields to the base by venting the systems level. Unfortunately Jaxo was on the systems level, so the Trooper had to make the difficult choice of saving the prisoners or Jaxo, before escaping.
The Trooper went to Voss to get soldiers who were stationed their in anticipation of a second invasion from the Empire. The Trooper first searched for proof of the Empire trying to invade. Havoc Squad discovered that the Empire acquired the bomb stolen by the traitors at Ord Mantell. After meeting with the Voss, and rescuing Voss soldiers, the Trooper traced the bomb to the Nightmare Lands. There, they killed the Sith and saved Voss, thus allowing the Republic soldiers based on Voss to fight in the war.
The Trooper is called back to Coruscant to answer charges made by a Senator. Upon arrival, Garza and Balker informed them the Senator was a puppet of the Empire, and the Trooper had to present proof to the Senate. After the corrupt Senator was dealt with, the Trooper was told Garza was on Corellia and that the final operations for Havoc Squad would be set up there.
On Corellia, the Trooper worked to prepare and gather forces scattered around Corellia for a final assault on the Bastion and defeat Rakton once and for all in the Bastion.
After gathering the man power, the troops fought their way through the Bastion's defenses until they reached the command center. The Trooper fought and defeated the general and after returning to Coruscant, received awards and accommodations for their efforts.