Following the loss of contact with Raala Ponchar, a spy for the Galactic Republic, Anakin Skywalker embarked on The Second Mission to Tatooine. He arrived in Mos Espa and assisted in eradicating a womp rat infestation plaguing the town. He also engaged Confederate battle droids that had overwhelmed Tatooine, but was ultimately captured by the bounty hunter Aurra Sing and the Dark Acolyte Saato. Imprisoned within Jabba's Palace, Anakin discovered Ponchar and uncovered a clandestine agreement between the CIS and Jabba. This agreement involved the production of a new type of battle droid utilizing lightsaber-resistant cortosis. After they successfully escaped, Anakin commandeered a skiff. Saato pursued him, leading to a duel above the Great Pit of Carkoon where Anakin emerged victorious, killing her.
In the aftermath of the Battle of Geonosis, the Jedi Council received concerning transmissions from Raala Ponchar, a moisture farmer residing on Tatooine. Ponchar reported multiple attacks on Tatooine's inhabitants carried out by an advanced type of battle droid. Tragically, communication with her was abruptly lost.
The Council, deeply concerned, summoned Anakin Skywalker. Fresh from his encounter with Count Dooku, Anakin believed he was prepared for any task. The Council briefed Anakin on the situation and tasked him with locating Raala Ponchar and gathering intelligence regarding these new battle droids on Tatooine.
Anakin's ship touched down near Mos Espa. As he made his way to the city, he had to contend with both womp rats and Tusken Raiders. Along the way, he also encountered several battle droids searching for Ponchar and overheard them mentioning someone called Mistress Saato.
Upon reaching Mos Espa, Anakin discovered the city was overrun by womp rats. He made inquiries and eventually found a mysterious woman who claimed that something was forcing the womp rats out of their burrows. She offered to share all she knew about Ponchar if he helped resolve the rat problem.
Venturing into the caves, Anakin discovered that anoobas were driving the rats from their nests. This puzzled him, as anoobas typically did not behave in this manner. He was compelled to eliminate six of the anoobas to restore calm among the rats.
As he exited the cave to return to the city, Anakin was confronted by Aurra Sing. He deduced that Sing was the cause of the problem, and he narrowly survived a thermal detonator she threw at him. Sing escaped, and Anakin had to fight his way through several bounty hunters to get back to Mos Espa.
After arriving back at Mos Espa, Anakin was informed that Watto, his former owner, might possess information regarding Ponchar. He went to Watto's shop and questioned him. Watto directed him toward the moisture farms located outside the city.
While traversing the Dune Sea, Anakin was compelled to rescue seven farmers who had been captured by Tusken Raiders. Upon reaching the moisture farms, he discovered they were in ruins. He also found some of the new battle droids. After defeating several of them and other battle droids, he questioned some of the surviving farmers. One of them, Bellek, Ponchar's employer, was hesitant to provide information due to fear of "a witch" who had led the Separatist attack on the farms. Anakin eventually discovered that the battle droids originated from Jabba the Hutt's palace.
After crossing the Jundland Wastes, battling bounty hunters and battle droids, Anakin arrived at Jabba's palace, where he once again faced Aurra. However, before he could apprehend the bounty hunter, the Dark Acolyte Saato appeared. Before Anakin could react, Saato used the Force to choke him into unconsciousness. Saato then ordered Anakin to be thrown into the dungeons.
Anakin regained consciousness in a cell inside Jabba's dungeons. Raala Ponchar was in the same cell. After using the Force to break free, and Ponchar located his lightsaber, Ponchar explained that the Separatists had contracted Jabba to transport a metal called cortosis for them. Cortosis was resistant to lightsabers, and the Separatists were incorporating it into their new battle droids.
Ponchar also revealed that other farmers were imprisoned in the dungeons. They decided to separate and rescue the farmers. Anakin navigated the dungeons, eliminating Jabba's guards and security droids while freeing the prisoners. Eventually, he freed everyone he could and escaped on a skiff.
Unfortunately for Anakin, Saato pursued him on a skiff of her own and shot his down near the Pit of Carkoon, the home of a sarlacc. Saato landed and activated her lightsabers, declaring that he would be fed to the sarlacc. A fierce lightsaber duel ensued. Despite Saato's combat skills, Anakin defeated and killed her.
Following his victory over Saato, Anakin reported his findings to his master and friend, Obi-Wan Kenobi. Kenobi was pleased but instructed Anakin to return to Coruscant immediately; the Separatists had launched an attack on the Galactic Capital.