The Bounty Hunter storyline begins on Hutta. The player joins up with a team of hunters, who are trying to use the player to get into the Great Hunt, a galactic-wide competition where hunters not only must hunt and kill a target, but kill a rival hunter tracking the same target.
The team consists of an old time hunter named Braden, a Nikto named Jory, and a young slicer named Mako. Braden, the team leader, is trying to negotiate with the local crime lord, Nemro the Hutt, to sponsor the hunter for the Great Hunt. However, a member of the Mandalorians named Tarro Blood, and rival for the Great Hunt, sabotages the hunter's chances of entering the Great Hunt by killing Braden and Jory in their base. The hunter arrives at the scene shortly before Mako, who is devastated at the death of Braden and Jory, the latter being a close friend and the former being a father figure. The hunter does jobs for Nemro and eventually gains the sponsorship of Nemro.
The entry into the Great Hunt leads the Bounty Hunter and Mako to the Imperial capital: Dromund Kaas. There they are informed that a large number of other hunters have arrived for the competition and have procured sponsorship; far too many, in fact, for the Hunt. After being assigned a handler by the name of Crysta, the Bounty Hunter is informed that each potential entrant must carry out three high-profile bounties on Dromund Kaas, as a means of thinning the herd of potentials. Afterward, the remaining elite bounty hunters will compete in a grand melee to determine the winner of the last entry into the Hunt.
The Bounty Hunter is given a series of targets: a Republic nobleman-turned-slave, the Sith daughter of an Imperial official and finally a mission into the dreaded Sith Dark Temple to retrieve proof of an officer's death. After completing these tasks the Bounty Hunter is entered into the "Grand Melee" and must fight the other challengers in an arena free-for-all match. The Bounty Hunter triumphs and is deemed worthy. Tarro Blood arrives soon after and protests this, citing that Mako fabricated much of the Bounty Hunter's qualifications. The Huntmaster (an aging Wookie presiding the event) deems that the skills of the Bounty Hunter are worthy of the Hunt even if his/her older exploits were exaggerated. Blood leaves, swearing to kill the player before the Great Hunt ends, as neither can kill the other before the hunt begins.
Crysta then informs the Bounty Hunter that a ship is needed to continue and that, in Mandalorian tradition, the ship should be stolen rather than bought. She directs the player to a D5-Mantis being used by a smuggler. Despite Blood having tipped off the Imperial authorities, the Bounty Hunter escapes, procuring the vessel in the process. Mako swears vengeance on Blood for his underhanded tactics even before the Hunt officially starts.
Once aboard, Crysta informs the crew that the first two targets for the Great Hunt have been decided for them. One lead is on Balmorra and the other on Nar Shaddaa. The Bounty Hunter is then given the choice as to which target to hunt down first.
Chapter 1 - The Great Hunt
The Balmorran Target for the Great Hunt is Admiral Ivernus, also known as "Admiral Untouchable," the reason being that he always oversees the conflict on the planet from his own starship. For that reason, the Bounty Hunter must lure him down to Balmorra if s/he has any chance of eliminating him. However, Crysta is unable to provide the Bounty Hunter with a friendly contact, though Mako managed to find out that Lieutenant Major Pirrell, one of Ivernus' "toadies", is in the market for a bounty hunter.
Down on Balmorra in Sobrik, the Bounty Hunter meets with Pirrell and Murghir, a dim Cathar entertainment gift from one of Pirrell's friends on Dromund Kaas. Pirrell reveals the reason why he posted the request for a bounty hunter in the first place: his wants his superior Colonel Sartius, whom he believes is incompetent yet is popular with the right people--including Admiral Ivernus, ousted from his seat and taken be Pirrell himself. He plans to do this by humiliating Sartius by having the Bounty Hunter create problems for Sartius that he is confident that he cannot solve in key points of interest such as the Okara Droid Factory, the local Colicoids, and the resistance fighters in the Balmorran Arms Factory.
Once all three points of interest have been taken care of, Pirrell happily reports to the Bounty Hunter that Sartius is placed under arrest and Ivernus is finally coming down to Balmorra. The Bounty Hunter seizes this opportunity to get within blaster range of the admiral.
The Bounty Hunter, Lieutenant Major Pirrell, and Murghir meet up with Admiral Ivernus at the Sobrik Spaceport. However, instead of giving Pirrell a promotion, Ivernus came down to Balmorra to execute him in person. Pirrell being in charge of intelligence, Ivernus sees him as a "worthless incompetent"--Colonel Sartius's failures are ultimately his own failures. However, Murghir reveals her true colors. She is the rival hunter in the Great Hunt intent on stealing the ultimate kill--her dim-witted nature was all a ruse. It becomes a three-way battle between the Bounty Hunter, Murghir, and Admiral Ivernus. After dealing with the admiral, his guards, the rival Cathar, and the terrified Lieutenant Major, the Bounty Hunter sets off for his/her next target.
The Bounty Hunter's target on Nar Shaddaa is called the Eidolon, a deadly, professional assassin with an equally ghastly reputation for being able to kill anybody for the right price. His primary employer is the Hutt Cartel. Gele'ren, a Twi'lek who works for the Hutt Cartel and hates the Eidolon, is the Bounty Hunter's friendly contact for this target.
Down on the planet, according to Gele'ren, the Eidolon recently started a security company--now everyone wants to buy from Eidolon Security, costing the Hutt Cartel valuable customers. Mako reunites with Anuli, an old friend who presumed her to be dead just before Braden took her down to Hutta. Gele'ren reveals that Eidolon Security's primary client is the Republic, supplying the Republic Army with billions of credits' worth of munitions every year. Destroying the crates of the munitions in the Corellian sector would cost Eidolon Security billions of credits, the first step in angering the Eidolon into going after the Bounty Hunter, which is exactly what s/he wants.
Gele'ren and the Bounty Hunter are discussing their next step in their plan when Mako and Anuli put two and two together and find out that the rival hunters, the Ugnaught Zargnor Clan, are building their new war droid in an empty building in the Druos sector (their old one blew up in the melee, killing everyone involved but themselves, who hid in the droid's armor). The Bounty Hunter finds the Ugnaughts in the empty building, still finishing their new war droid.
After dealing with the Zargnor Clan, Anuli and Mako discuss with the Bounty Hunter about Anuli coming along once this is over, since he has helped out a lot. After resolving the issue, the next step in provoking the Eidolon is to get every one of his confidential record into the public HoloNet, where anyone can access. Anuli reports that the Eidolon's HoloNet transceivers are in the Network Access Sector, heavily guarded and encrypted. The Bounty Hunter must track down Zee, a Bith engineer who has the access codes to the Eidolon's network. Because Zee is working for Nebula Communications, s/he can track him down by finding a security officer, who reveals that Zee is at the Imperial spaceport, preparing for departure.
Chapter 2 - The Price of Fame
Chapter 3 - Public Enemy