Shortly after the Battle of Naboo, Yaddle was involved in negotiations with another militant group known as the Red Iaro. Some viewed the group as a terrorist organization trying to usurp the legitimate rulers of Lannik. Even one of Yaddle's contemporaries, Jedi Master Even Piell, had dealt with them before, losing an eye in the process. After the Battle of Naboo, the Jedi were invited to participate in another round of peace negotiations on the planet of Malastare between the ruling Lannik prince, R'cardo Sooflie IX, and the current Red Iaro leader, known as Myk'Chur Finux Zug.

Yaddle joined Jedi Masters Mace Windu, Even Piell, Depa Billaba, Plo Koon, Ki-Adi-Mundu, and his Padawan, A'Sharad Hett as emissaries to Malastare. Unfortunately, the Red Iaro had no intention of negotiating. The meeting was simply a ruse to lure Prince R'cardo out into the open and assassinate both him and the Jedi. When a speeder crash failed to take out Yaddle and the Jedi, the terrorist leader unleashed two feral aak dogs against the Jedi. However, during his escape attempt, he flew his jetpack into the path of an oncoming podracer and was sucked into the engine. With the threat of the Red Iaro concluded, Yaddle joined the Jedi in returning to Coruscant.

Jedi Master Yaddle's final mission took place during the Separatist crisis shortly before the Clone Wars. This time, the threat involved one man, a crime lord by the name of Granta Omega. It is unknown why Granta Omega harbored such hatred towards the Jedi, only that it developed sometime during his youth. As he grew in power he used the resources at his disposal to eliminate as many of them as possible. Omega set up a number of elaborate traps and schemes and even took out bounties on prominent Jedi Masters.

Unfortunately for Jedi Master Yaddle, she soon found herself in his crosshairs. Using the political turmoil of the planet Mawan, where a civil war had been raging for the previous decade, Omega lured Jedi Master Obi-Wan Kenobi and Anakin Skywalker into a trap, kidnapping young Skywalker in the process. Demanding to meet with Master Yaddle, the diminutive Jedi complied. On Mawan, Yaddle discovered Omega's plans to unleash a chemical bomb filled with dihexalon gas on the city of Naatan. Sacrificing herself to protect the city, Yaddle used the Force to envelop the bomb causing it to implode and drawing the poison inwards.