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 devestated 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 hunter travels to Dromund Kaas, the Imperial captial, to enter the Great Hunt.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 Tarro Blood having tipped off the Imperial authorities, the Bounty Hunter escapes, procuring the vessel in the process.
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.