Invasion of Ossus

In 3636 BBY, the Eternal Empire under led by the former Sith Emperor Vitiate attacked both the Sith Empire and the Galactic Republic. This onslaught forced many surviving members of the Jedi Order into hiding. By 3630 BBY, Jedi and Sith led by the Eternal Alliance's Commander initiated a revolt against the Eternal Empire that would culminate with the death of the former Sith Emperor.

During the conflict, Master Gnost-Dural's vision for Ossus was to help the colonists grow crops in order to better support them while Jedi Knight Tau Idair wanted to send out teams to find surviving Jedi. However, Gnost-Dural did not take such action as to ensure that the Jedi remained hidden from the Sith. Sometime after the end of the war against Zakuul, the Sith Empire learned that Jedi Master Gnost-Dural was alive hiding on the Jedi farming colony on Ossus. The Empire sent an attack force to the planet under the command of Dark Council member Darth Malora, while Republic General Daeruun sought to reinforce the colony before the Sith could destroy it. With the Eternal Alliance's waning power in the galaxy, they feared a conflict with both main factions, and decided to side with the Jedi and Republic, and the Alliance Commander arrived to assist in the defense of Ossus.

After Ossus both the Republic and the Sith Empire learned that Darth Malgus had survived his supposed death above Ilum. Darth Malora's seat on the Dark Council was vacated after Malgus overtook her operation on the planet. Additional Republic and Imperial forces arrived at the planet including multiple Valor-class cruisers, Thranta-class corvettes, and Harrower-class dreadnaughts, along with their escort fighters.

The choices that were made by the player in the Iokath expansion determine whether it is Darth Acina or Darth Vowrawn who appear as Empress/Emperor in the Sith storyline. The player's class also determines which companions the player reunites with during the Ossus storyline: the Sith Warrior class with Jaesa Willsaam, the Jedi Knight class with Doc, the Jedi Consular class with Nadia Grell, and the Sith Inquisitor class with Khem Val. Imperial classes also encounter Moff Pyron, a non-companion from the Inquisitor storyline.

At the end of the storyline, the fate of Gnost-Dural differs between factions. If the player sides with the Empire, they can take Gnost-Dural as a prisoner for Light Side points or let Malgus kill him for Dark Side points. If the player sides with the Republic, Malgus will seriously wound Gnost-Dural and leave him in the library. Idair and the player will find a barely alive Dural and take him to Doc, so he can save him.

Additionally, the storyline deals with the farming data that could provide food for either faction amidst the galactic resource crisis. A loyalist player retrieve the data for their faction while a saboteur player fakes the data's destruction and hands it over to the opposing faction.