During the Clone Wars, Atai Molec and Count Dooku spoke with Commander Darts D'Nar about his last shipment of Kiros's colonists. Molec was surprised that D'Nar had not left yet. As Republic Jedi General Obi-Wan Kenobi entered to speak with D'Nar, Molec growled when Dooku introduced him to Kenobi.
As Molec was about to whip one his slaves, he was stopped by a slave. He then saw the slave's master in Zygerrian armor and that he flew one of their ships. At first, Molec was distrusful of him when he demanded to speak to the Queen about Bruno Denturri. However, Molec brought in the man known as Lars Quell before the queen. Molec was then told that a man in Zygerrian armor had tried to free one of the enslaved colonists. Molec then realized that it was Kenobi. Molec then brought Kenobi before the Queen to punish him for the Jedi's crimes against their empire. However, Molec, the Queen and their guards were then attack by Quell and his slave, who revealed themselves to be Anakin Skywalker and his apprentice, Ahsoka Tano. Though Molec was knocked down by Tano, the Queen and their guards were eventually able to subdue the Jedi.
Later, Molec visited a caged Tano and revealed that the Queen had promised that after Skywalker was tamed, Tano would be his slave to do with whatever he desired. As an act of defiance, Tano telekentically pushed Molec off a precipice, nearly sending him falling to his death. In retaliation, Molec electrocuted Tano several times with the shock collar she was wearing as a slave.
Molec then invited Dooku to Zygerria to speak with the Queen about her defiance in not killing Skywalker. When the Queen refused, Molec agreed with Dooku about killing the Jedi (except for Tano) and that Scintel was unfit to be queen. Molec then stood by as Dooku Force-choked her.
- Star Wars: The Clone Wars – "Kidnapped" (First appearance) (Appears in hologram)
- Star Wars: The Clone Wars – "Slaves of the Republic"
- Star Wars: The Clone Wars – "Escape from Kadavo"