The game ups the level cap from 50 to 55. It adds a new level 55 Operation, another mini-Operation, a level 55 nightmare mode-version of the Terror From Beyond Operation, and level 55 hard mode for several Flashpoints.
It also adds a whole new campaign where Toborro has seized the leadership of the Hutt Cartel and uses his new acquired powers to inhabit the planet of Makeb to harvest its very valuable mineral isotope-5. The Regulators, Makeb's defense force, are payed off to defend his mining operations.
As it turns out, isotope-5 can only be found in Makeb's core, and mining the mineral has destabilized the planet. Blinded by greed Toborro keeps his operations going, even though it can threaten its nature and inhabitants.
The Republic invades, with help of the Jedi Order, the planet to end any mining operations, rescue Makeb's citizens and bring Toborro to justice. The player together with Shalim Avesta, leader of the Makeb resistance, rescue a geophysicist and niece to Shalim. Lemda, along with Hutt dr. Juvard Illip Oggurobb are both rescued in order to try to find a way to stop the madness.
But the Hutt Cartel hasn't been sitting idle either, Toborro has build a giant space ship named The Ark to flee the planet together with the other Cartel leaders, his precious isotope-5 and if possible, his soldiers. Eventually the Republic ceases The Ark and kills Toborro. The Ark is used to rescue Makeb's citizens and move everyone off planet. The other Hutt Cartel leaders are ordered to fund a new home for the Makeb residents, since Makeb isn't suitable to live upon anymore.
Meanwhile, Darth Marr's Imperial troopers have somehow prevented the planet's destruction and establish a presence on the planet. Thousands of civilians thought to be dead, appear to be alive and well. The Republic is once again sent back to rescue the remaining people.